Sequence Compression Benchmark

Commands

This page lists all actual benchmarked commands. The commands are templates, parts in curly brackets were substituted before running them. Note that many compressors were used via wrappers.

Jump to: 2bit ac alapy bcm beetl blast brieflz brotli bsc bzip2 cmix copy dcom dlim dnax dsrc fastqz fqs fqzcomp geco geco2 geco3 gtz gzip harc jarvis kic leon lfastqc lfqc lizard lz4 lzop lzturbo mfc minicom naf nakamichi nuht pbzip2 pigz pfish quip snzip spring uht xm xz zpaq zpipe zstd

2bit

DNA compression
2bit-compress.pl --out {OUT}
RNA compression
2bit-compress.pl --out {OUT} --rna
DNA decompression
2bit-decompress.pl --in '{IN}'
RNA decompression
2bit-decompress.pl --in '{IN}' --rna
DNA compression, wrapper only
2bit-compress.pl --out {OUT} --wrapper-only
RNA compression, wrapper only
2bit-compress.pl --out {OUT} --rna --wrapper-only
DNA decompression, wrapper only
2bit-decompress.pl --in '{IN}' --wrapper-only
RNA decompression, wrapper only
2bit-decompress.pl --in '{IN}' --rna --wrapper-only

ac

Protein compression
ac-fa-1ac-fa-compress.pl --out {OUT} --level 1
ac-fa-2ac-fa-compress.pl --out {OUT} --level 2
ac-fa-3ac-fa-compress.pl --out {OUT} --level 3
ac-fa-4ac-fa-compress.pl --out {OUT} --level 4
ac-fa-5ac-fa-compress.pl --out {OUT} --level 5
ac-fa-6ac-fa-compress.pl --out {OUT} --level 6
ac-fa-7ac-fa-compress.pl --out {OUT} --level 7
ac-seq-1ac-seq-compress.pl --out {OUT} --level 1
ac-seq-2ac-seq-compress.pl --out {OUT} --level 2
ac-seq-3ac-seq-compress.pl --out {OUT} --level 3
ac-seq-4ac-seq-compress.pl --out {OUT} --level 4
ac-seq-5ac-seq-compress.pl --out {OUT} --level 5
ac-seq-6ac-seq-compress.pl --out {OUT} --level 6
ac-seq-7ac-seq-compress.pl --out {OUT} --level 7
Protein decompression
ac-fa-*ac-fa-decompress.pl --in '{IN}'
ac-seq-*ac-seq-decompress.pl --in '{IN}'
Protein compression, wrapper only
wrap-ac-faac-fa-compress.pl --out {OUT} --level 1 --wrapper-only
wrap-ac-seqac-seq-compress.pl --out {OUT} --level 1 --wrapper-only
Protein decompression, wrapper only
wrap-ac-faac-fa-decompress.pl --in '{IN}' --wrapper-only
wrap-ac-seqac-seq-decompress.pl --in '{IN}' --wrapper-only

alapy

DNA compression
alapy-falapy-compress.pl --out {OUT} --level f
alapy-malapy-compress.pl --out {OUT} --level m
alapy-balapy-compress.pl --out {OUT} --level b
RNA compression
alapy-falapy-compress.pl --out {OUT} --level f --rna
alapy-malapy-compress.pl --out {OUT} --level m --rna
alapy-balapy-compress.pl --out {OUT} --level b --rna
DNA decompression
alapy-*alapy-decompress.pl --in '{IN}'
RNA decompression
alapy-*alapy-decompress.pl --in '{IN}' --rna
DNA compression, wrapper only
wrap-alapyalapy-compress.pl --out {OUT} --level f --wrapper-only
RNA compression, wrapper only
wrap-alapyalapy-compress.pl --out {OUT} --level f --rna --wrapper-only
DNA decompression, wrapper only
wrap-alapyalapy-decompress.pl --in '{IN}' --wrapper-only
RNA decompression, wrapper only
wrap-alapyalapy-decompress.pl --in '{IN}' --rna --wrapper-only

bcm

Compression
bcm-b16bcm-compress.pl --b 16 --out {OUT}
bcm-b128bcm-compress.pl --b 128 --out {OUT}
bcm-b1024bcm-compress.pl --b 1024 --out {OUT}
bcm-b2047bcm-compress.pl --b 2047 --out {OUT}
Decompression
bcm-decompress.pl '{IN}'

beetl

DNA compression
beetl-b50-zst1beetl-compress.pl --out {OUT} --read-length 50 --algorithm BCR --compressor zstd1
beetl-b200-zst1beetl-compress.pl --out {OUT} --read-length 200 --algorithm BCR --compressor zstd1
beetl-b500-zst1beetl-compress.pl --out {OUT} --read-length 500 --algorithm BCR --compressor zstd1
beetl-b50-zst22beetl-compress.pl --out {OUT} --read-length 50 --algorithm BCR --compressor zstd22
beetl-b200-zst22beetl-compress.pl --out {OUT} --read-length 200 --algorithm BCR --compressor zstd22
beetl-b500-zst22beetl-compress.pl --out {OUT} --read-length 500 --algorithm BCR --compressor zstd22
RNA compression
beetl-b50-zst1beetl-compress.pl --out {OUT} --read-length 50 --algorithm BCR --compressor zstd1 --rna
beetl-b200-zst1beetl-compress.pl --out {OUT} --read-length 200 --algorithm BCR --compressor zstd1 --rna
beetl-b500-zst1beetl-compress.pl --out {OUT} --read-length 500 --algorithm BCR --compressor zstd1 --rna
beetl-b50-zst22beetl-compress.pl --out {OUT} --read-length 50 --algorithm BCR --compressor zstd22 --rna
beetl-b200-zst22beetl-compress.pl --out {OUT} --read-length 200 --algorithm BCR --compressor zstd22 --rna
beetl-b500-zst22beetl-compress.pl --out {OUT} --read-length 500 --algorithm BCR --compressor zstd22 --rna
DNA decompression
beetl-*beetl-decompress.pl --in '{IN}'
RNA decompression
beetl-*beetl-decompress.pl --in '{IN}' --rna
DNA compression, wrapper only
wrap-beetlbeetl-compress.pl --out {OUT} --read-length 500 --algorithm BCR --compressor zstd1 --wrapper-only
RNA compression, wrapper only
wrap-beetlbeetl-compress.pl --out {OUT} --read-length 500 --algorithm BCR --compressor zstd1 --rna --wrapper-only
DNA decompression, wrapper only
wrap-beetlbeetl-decompress.pl --in '{IN}' --wrapper-only
RNA decompression, wrapper only
wrap-beetlbeetl-decompress.pl --in '{IN}' --rna --wrapper-only

blast

DNA compression
blast-compress.pl --out {OUT}
RNA compression
blast-compress.pl --out {OUT} --rna
Protein compression
blast-compress.pl --out {OUT} --protein
DNA & protein decompression
blast-decompress.pl --in '{IN}'
RNA decompression
blast-decompress.pl --in '{IN}' --rna
DNA compression, wrapper only
blast-compress.pl --out {OUT} --wrapper-only
RNA compression, wrapper only
blast-compress.pl --out {OUT} --rna --wrapper-only
Protein compression, wrapper only
blast-compress.pl --out {OUT} --protein --wrapper-only
DNA & protein decompression, wrapper only
blast-decompress.pl --in '{IN}' --wrapper-only
RNA decompression, wrapper only
blast-decompress.pl --in '{IN}' --rna --wrapper-only

brieflz

Compression
brieflz-1blzpack -1 /dev/stdin {OUT}
brieflz-2blzpack -2 /dev/stdin {OUT}
brieflz-3blzpack -3 /dev/stdin {OUT}
brieflz-4blzpack -4 /dev/stdin {OUT}
brieflz-5blzpack -5 /dev/stdin {OUT}
brieflz-6blzpack -6 /dev/stdin {OUT}
brieflz-6-3600mblzpack -6 -b3600m /dev/stdin {OUT}
brieflz-7blzpack -7 /dev/stdin {OUT}
brieflz-8blzpack -8 /dev/stdin {OUT}
brieflz-9blzpack -9 /dev/stdin {OUT}
brieflz-9-3600mblzpack -9 -b3600m /dev/stdin {OUT}
brieflz-optblzpack --optimal /dev/stdin {OUT}
Decompression
brieflz-#blzpack -d {IN} /dev/stdout
brieflz-#-3600mblzpack -d -b3600m {IN} /dev/stdout

brotli

Compression
brotli-0brotli -q 0 -c >{OUT}
brotli-1brotli -q 1 -c >{OUT}
brotli-2brotli -q 2 -c >{OUT}
brotli-3brotli -q 3 -c >{OUT}
brotli-4brotli -q 4 -c >{OUT}
brotli-5brotli -q 5 -c >{OUT}
brotli-6brotli -q 6 -c >{OUT}
brotli-7brotli -q 7 -c >{OUT}
brotli-8brotli -q 8 -c >{OUT}
brotli-9brotli -q 9 -c >{OUT}
brotli-10brotli -q 10 -c >{OUT}
brotli-11brotli -q 11 -c >{OUT}
Compression with undocumented settings
brotli-11w30brotli -q 11 --large_window=30 -c >{OUT}
Decompression
brotli -dc '{IN}'

bsc

Compression
bsc-b16cfe1bsc-compress.pl --b 16 --c f --e 1 --out {OUT}
bsc-b128cfe1bsc-compress.pl --b 128 --c f --e 1 --out {OUT}
bsc-b1024cfe1bsc-compress.pl --b 1024 --c f --e 1 --out {OUT}
bsc-b16cfe2bsc-compress.pl --b 16 --c f --e 2 --out {OUT}
bsc-b128cfe2bsc-compress.pl --b 128 --c f --e 2 --out {OUT}
bsc-b1024cfe2bsc-compress.pl --b 1024 --c f --e 2 --out {OUT}
Decompression
bsc-decompress.pl '{IN}'

bzip2

Compression
bzip2-1bzip2 -cz1 >{OUT}
bzip2-2bzip2 -cz2 >{OUT}
bzip2-3bzip2 -cz3 >{OUT}
bzip2-4bzip2 -cz4 >{OUT}
bzip2-5bzip2 -cz5 >{OUT}
bzip2-6bzip2 -cz6 >{OUT}
bzip2-7bzip2 -cz7 >{OUT}
bzip2-8bzip2 -cz8 >{OUT}
bzip2-9bzip2 -cz9 >{OUT}
Decompression
bzip2 -dc '{IN}'

cmix

Compression
cmix-compress.pl --out {OUT}
Decompression
cmix-decompress.pl '{IN}'

copy

Compression
copy-catcat >{OUT}
copy-pigz-0-1tpigz -p 1 -c -0 >{OUT}
copy-pigz-0-4tpigz -p 4 -c -0 >{OUT}
Decompression
copy-catcat '{IN}'
copy-pigz-0-1tpigz -dc '{IN}'
copy-pigz-0-4tpigz -dc '{IN}'

dcom

Compression
dcom-9dcom-compress.pl --out {OUT} --level 9
dcom-10dcom-compress.pl --out {OUT} --level 10
dcom-11dcom-compress.pl --out {OUT} --level 11
dcom-12dcom-compress.pl --out {OUT} --level 12
dcom-13dcom-compress.pl --out {OUT} --level 13
dcom-14dcom-compress.pl --out {OUT} --level 14
dcom-15dcom-compress.pl --out {OUT} --level 15
dcom-16dcom-compress.pl --out {OUT} --level 16
dcom-17dcom-compress.pl --out {OUT} --level 17
dcom-18dcom-compress.pl --out {OUT} --level 18
dcom-19dcom-compress.pl --out {OUT} --level 19
dcom-20dcom-compress.pl --out {OUT} --level 20
dcom-21dcom-compress.pl --out {OUT} --level 21
dcom-22dcom-compress.pl --out {OUT} --level 22
dcom-23dcom-compress.pl --out {OUT} --level 23
dcom-24dcom-compress.pl --out {OUT} --level 24
dcom-25dcom-compress.pl --out {OUT} --level 25
dcom-26dcom-compress.pl --out {OUT} --level 26
dcom-27dcom-compress.pl --out {OUT} --level 27
dcom-28dcom-compress.pl --out {OUT} --level 28
dcom-29dcom-compress.pl --out {OUT} --level 29
dcom-30dcom-compress.pl --out {OUT} --level 30
Decompression
dcom-decompress.pl --in '{IN}'
Compression, wrapper only
dcom-compress.pl --out {OUT} --level 9 --wrapper-only
Decompression, wrapper only
dcom-decompress.pl --in '{IN}' --wrapper-only

dlim

DNA compression
dlim-compress.pl --out {OUT}
RNA compression
dlim-compress.pl --out {OUT} --rna
DNA decompression
dlim-decompress.pl --in '{IN}'
RNA decompression
dlim-decompress.pl --in '{IN}' --rna

dnax

DNA compression
dnax-0dnax-compress.pl --out {OUT} --preset 0
dnax-1dnax-compress.pl --out {OUT} --preset 1
dnax-2dnax-compress.pl --out {OUT} --preset 2
dnax-3dnax-compress.pl --out {OUT} --preset 3
RNA compression
dnax-0dnax-compress.pl --out {OUT} --preset 0 --rna
dnax-1dnax-compress.pl --out {OUT} --preset 1 --rna
dnax-2dnax-compress.pl --out {OUT} --preset 2 --rna
dnax-3dnax-compress.pl --out {OUT} --preset 3 --rna
DNA decompression
dnax-*dnax-decompress.pl --in '{IN}'
RNA decompression
dnax-*dnax-decompress.pl --in '{IN}' --rna
DNA compression, wrapper only
wrap-dnaxdnax-compress.pl --out {OUT} --preset 0 --wrapper-only
RNA compression, wrapper only
wrap-dnaxdnax-compress.pl --out {OUT} --preset 0 --rna --wrapper-only
DNA decompression, wrapper only
wrap-dnaxdnax-decompress.pl --in '{IN}' --wrapper-only
RNA decompression, wrapper only
wrap-dnaxdnax-decompress.pl --in '{IN}' --rna --wrapper-only

dsrc

DNA compression
dsrc-m0-1tdsrc-compress.pl --out {OUT} --level 0 --buffer-size 8 --threads 1
dsrc-m1-1tdsrc-compress.pl --out {OUT} --level 2 --buffer-size 64 --threads 1
dsrc-m2-1tdsrc-compress.pl --out {OUT} --level 3 --buffer-size 256 --threads 1
dsrc-m0-4tdsrc-compress.pl --out {OUT} --level 0 --buffer-size 8 --threads 4
dsrc-m1-4tdsrc-compress.pl --out {OUT} --level 2 --buffer-size 64 --threads 4
dsrc-m2-4tdsrc-compress.pl --out {OUT} --level 3 --buffer-size 256 --threads 4
RNA compression
dsrc-m0-1tdsrc-compress.pl --out {OUT} --level 0 --buffer-size 8 --threads 1 --rna
dsrc-m1-1tdsrc-compress.pl --out {OUT} --level 2 --buffer-size 64 --threads 1 --rna
dsrc-m2-1tdsrc-compress.pl --out {OUT} --level 3 --buffer-size 256 --threads 1 --rna
dsrc-m0-4tdsrc-compress.pl --out {OUT} --level 0 --buffer-size 8 --threads 4 --rna
dsrc-m1-4tdsrc-compress.pl --out {OUT} --level 2 --buffer-size 64 --threads 4 --rna
dsrc-m2-4tdsrc-compress.pl --out {OUT} --level 3 --buffer-size 256 --threads 4 --rna
DNA decompression
dsrc-*-1tdsrc-decompress.pl --in '{IN}' --threads 1
dsrc-*-4tdsrc-decompress.pl --in '{IN}' --threads 4
RNA decompression
dsrc-*-1tdsrc-decompress.pl --in '{IN}' --threads 1 --rna
dsrc-*-4tdsrc-decompress.pl --in '{IN}' --threads 4 --rna
DNA compression, wrapper only
wrap-dsrcdsrc-compress.pl --out {OUT} --level 0 --buffer-size 8 --threads 1 --wrapper-only
RNA compression, wrapper only
wrap-dsrcdsrc-compress.pl --out {OUT} --level 0 --buffer-size 8 --threads 1 --rna --wrapper-only
DNA decompression, wrapper only
wrap-dsrcdsrc-decompress.pl --in '{IN}' --threads 1 --wrapper-only
RNA decompression, wrapper only
wrap-dsrcdsrc-decompress.pl --in '{IN}' --threads 1 --rna --wrapper-only

fastqz

DNA compression
fastqz-fastfastqz-compress.pl --out {OUT} --mode fast --read-length 4000
fastqz-slowfastqz-compress.pl --out {OUT} --mode slow --read-length 4000
RNA compression
fastqz-fastfastqz-compress.pl --out {OUT} --mode fast --read-length 4000 --rna
fastqz-slowfastqz-compress.pl --out {OUT} --mode slow --read-length 4000 --rna
DNA decompression
fastqz-fastfastqz-decompress.pl --in '{IN}' --mode fast
fastqz-slowfastqz-decompress.pl --in '{IN}' --mode slow
RNA decompression
fastqz-fastfastqz-decompress.pl --in '{IN}' --mode fast --rna
fastqz-slowfastqz-decompress.pl --in '{IN}' --mode slow --rna
DNA compression, wrapper only
wrap-fastqzfastqz-compress.pl --out {OUT} --mode fast --read-length 4000 --wrapper-only
RNA compression, wrapper only
wrap-fastqzfastqz-compress.pl --out {OUT} --mode fast --read-length 4000 --rna --wrapper-only
DNA decompression, wrapper only
wrap-fastqzfastqz-decompress.pl --in '{IN}' --mode fast --wrapper-only
RNA decompression, wrapper only
wrap-fastqzfastqz-decompress.pl --in '{IN}' --mode fast --rna --wrapper-only

fqs

DNA compression
fqs-1tfqsqueezer-compress.pl --out {OUT} --read-length 4000 --threads 1
fqs-4tfqsqueezer-compress.pl --out {OUT} --read-length 4000 --threads 4
DNA decompression
fqs-*fqsqueezer-decompress.pl --in '{IN}'
DNA compression, wrapper only
wrap-fqsfqsqueezer-compress.pl --out {OUT} --read-length 250 --threads 1 --wrapper-only
DNA decompression, wrapper only
wrap-fqsfqsqueezer-decompress.pl --in '{IN}' --wrapper-only

fqzcomp

DNA compression
fqzcomp-1fqzcomp-compress.pl --out {OUT} --read-length 4000 -s 1
fqzcomp-2fqzcomp-compress.pl --out {OUT} --read-length 4000 -s 2
fqzcomp-3fqzcomp-compress.pl --out {OUT} --read-length 4000 -s 3
fqzcomp-4fqzcomp-compress.pl --out {OUT} --read-length 4000 -s 4
fqzcomp-5fqzcomp-compress.pl --out {OUT} --read-length 4000 -s 5
fqzcomp-6fqzcomp-compress.pl --out {OUT} --read-length 4000 -s 6
fqzcomp-7fqzcomp-compress.pl --out {OUT} --read-length 4000 -s 7
fqzcomp-8fqzcomp-compress.pl --out {OUT} --read-length 4000 -s 8
RNA compression
fqzcomp-1fqzcomp-compress.pl --out {OUT} --read-length 4000 -s 1 --rna
fqzcomp-2fqzcomp-compress.pl --out {OUT} --read-length 4000 -s 2 --rna
fqzcomp-3fqzcomp-compress.pl --out {OUT} --read-length 4000 -s 3 --rna
fqzcomp-4fqzcomp-compress.pl --out {OUT} --read-length 4000 -s 4 --rna
fqzcomp-5fqzcomp-compress.pl --out {OUT} --read-length 4000 -s 5 --rna
fqzcomp-6fqzcomp-compress.pl --out {OUT} --read-length 4000 -s 6 --rna
fqzcomp-7fqzcomp-compress.pl --out {OUT} --read-length 4000 -s 7 --rna
fqzcomp-8fqzcomp-compress.pl --out {OUT} --read-length 4000 -s 8 --rna
DNA decompression
fqzcomp-*fqzcomp-decompress.pl --in '{IN}'
RNA decompression
fqzcomp-*fqzcomp-decompress.pl --in '{IN}' --rna
DNA compression, wrapper only
wrap-fqzcompfqzcomp-compress.pl --out {OUT} --read-length 4000 -s 1 --wrapper-only
RNA compression, wrapper only
wrap-fqzcompfqzcomp-compress.pl --out {OUT} --read-length 4000 -s 1 --rna --wrapper-only
DNA decompression, wrapper only
wrap-fqzcompfqzcomp-decompress.pl --in '{IN}' --wrapper-only
RNA decompression, wrapper only
wrap-fqzcompfqzcomp-decompress.pl --in '{IN}' --rna --wrapper-only

geco

Compression
geco-2-zs1geco-compress.pl --level 2 --compressor zstd1 --out {OUT}
geco-3-zs1geco-compress.pl --level 3 --compressor zstd1 --out {OUT}
geco-4-zs1geco-compress.pl --level 4 --compressor zstd1 --out {OUT}
geco-5-zs1geco-compress.pl --level 5 --compressor zstd1 --out {OUT}
geco-6-zs1geco-compress.pl --level 6 --compressor zstd1 --out {OUT}
geco-7-zs1geco-compress.pl --level 7 --compressor zstd1 --out {OUT}
geco-8-zs1geco-compress.pl --level 8 --compressor zstd1 --out {OUT}
geco-9-zs1geco-compress.pl --level 9 --compressor zstd1 --out {OUT}
geco-10-zs1geco-compress.pl --level 10 --compressor zstd1 --out {OUT}
geco-2-zs22geco-compress.pl --level 2 --compressor zstd22 --out {OUT}
geco-3-zs22geco-compress.pl --level 3 --compressor zstd22 --out {OUT}
geco-4-zs22geco-compress.pl --level 4 --compressor zstd22 --out {OUT}
geco-5-zs22geco-compress.pl --level 5 --compressor zstd22 --out {OUT}
geco-6-zs22geco-compress.pl --level 6 --compressor zstd22 --out {OUT}
geco-7-zs22geco-compress.pl --level 7 --compressor zstd22 --out {OUT}
geco-8-zs22geco-compress.pl --level 8 --compressor zstd22 --out {OUT}
geco-9-zs22geco-compress.pl --level 9 --compressor zstd22 --out {OUT}
geco-10-zs22geco-compress.pl --level 10 --compressor zstd22 --out {OUT}
Decompression
geco-*geco-decompress.pl --in '{IN}'
Compression, wrapper only
wrap-gecogeco-compress.pl --level 2 --compressor zstd1 --out {OUT} --wrapper-only
Decompression, wrapper only
wrap-gecogeco-decompress.pl --in '{IN}' --wrapper-only

geco2

Compression
geco2-1-zs1geco2-compress.pl --level 1 --compressor zstd1 --out {OUT}
geco2-2-zs1geco2-compress.pl --level 2 --compressor zstd1 --out {OUT}
geco2-3-zs1geco2-compress.pl --level 3 --compressor zstd1 --out {OUT}
geco2-4-zs1geco2-compress.pl --level 4 --compressor zstd1 --out {OUT}
geco2-5-zs1geco2-compress.pl --level 5 --compressor zstd1 --out {OUT}
geco2-6-zs1geco2-compress.pl --level 6 --compressor zstd1 --out {OUT}
geco2-7-zs1geco2-compress.pl --level 7 --compressor zstd1 --out {OUT}
geco2-8-zs1geco2-compress.pl --level 8 --compressor zstd1 --out {OUT}
geco2-9-zs1geco2-compress.pl --level 9 --compressor zstd1 --out {OUT}
geco2-10-zs1geco2-compress.pl --level 10 --compressor zstd1 --out {OUT}
geco2-11-zs1geco2-compress.pl --level 11 --compressor zstd1 --out {OUT}
geco2-12-zs1geco2-compress.pl --level 12 --compressor zstd1 --out {OUT}
geco2-13-zs1geco2-compress.pl --level 13 --compressor zstd1 --out {OUT}
geco2-14-zs1geco2-compress.pl --level 14 --compressor zstd1 --out {OUT}
geco2-15-zs1geco2-compress.pl --level 15 --compressor zstd1 --out {OUT}
geco2-1-zs22geco2-compress.pl --level 1 --compressor zstd22 --out {OUT}
geco2-2-zs22geco2-compress.pl --level 2 --compressor zstd22 --out {OUT}
geco2-3-zs22geco2-compress.pl --level 3 --compressor zstd22 --out {OUT}
geco2-4-zs22geco2-compress.pl --level 4 --compressor zstd22 --out {OUT}
geco2-5-zs22geco2-compress.pl --level 5 --compressor zstd22 --out {OUT}
geco2-6-zs22geco2-compress.pl --level 6 --compressor zstd22 --out {OUT}
geco2-7-zs22geco2-compress.pl --level 7 --compressor zstd22 --out {OUT}
geco2-8-zs22geco2-compress.pl --level 8 --compressor zstd22 --out {OUT}
geco2-9-zs22geco2-compress.pl --level 9 --compressor zstd22 --out {OUT}
geco2-10-zs22geco2-compress.pl --level 10 --compressor zstd22 --out {OUT}
geco2-11-zs22geco2-compress.pl --level 11 --compressor zstd22 --out {OUT}
geco2-12-zs22geco2-compress.pl --level 12 --compressor zstd22 --out {OUT}
geco2-13-zs22geco2-compress.pl --level 13 --compressor zstd22 --out {OUT}
geco2-14-zs22geco2-compress.pl --level 14 --compressor zstd22 --out {OUT}
geco2-15-zs22geco2-compress.pl --level 15 --compressor zstd22 --out {OUT}
Decompression
geco2-*geco2-decompress.pl --in '{IN}'
Compression, wrapper only
wrap-geco2geco2-compress.pl --level 1 --compressor zstd1 --out {OUT} --wrapper-only
Decompression, wrapper only
wrap-geco2geco2-decompress.pl --in '{IN}' --wrapper-only

geco3

Compression
geco3-1-zs1geco3-compress.pl --level 1 --compressor zstd1 --out {OUT}
geco3-2-zs1geco3-compress.pl --level 2 --compressor zstd1 --out {OUT}
geco3-3-zs1geco3-compress.pl --level 3 --compressor zstd1 --out {OUT}
geco3-4-zs1geco3-compress.pl --level 4 --compressor zstd1 --out {OUT}
geco3-5-zs1geco3-compress.pl --level 5 --compressor zstd1 --out {OUT}
geco3-6-zs1geco3-compress.pl --level 6 --compressor zstd1 --out {OUT}
geco3-7-zs1geco3-compress.pl --level 7 --compressor zstd1 --out {OUT}
geco3-8-zs1geco3-compress.pl --level 8 --compressor zstd1 --out {OUT}
geco3-9-zs1geco3-compress.pl --level 9 --compressor zstd1 --out {OUT}
geco3-10-zs1geco3-compress.pl --level 10 --compressor zstd1 --out {OUT}
geco3-11-zs1geco3-compress.pl --level 11 --compressor zstd1 --out {OUT}
geco3-12-zs1geco3-compress.pl --level 12 --compressor zstd1 --out {OUT}
geco3-13-zs1geco3-compress.pl --level 13 --compressor zstd1 --out {OUT}
geco3-14-zs1geco3-compress.pl --level 14 --compressor zstd1 --out {OUT}
geco3-15-zs1geco3-compress.pl --level 15 --compressor zstd1 --out {OUT}
geco3-16-zs1geco3-compress.pl --level 16 --compressor zstd1 --out {OUT}
geco3-1-zs22geco3-compress.pl --level 1 --compressor zstd22 --out {OUT}
geco3-2-zs22geco3-compress.pl --level 2 --compressor zstd22 --out {OUT}
geco3-3-zs22geco3-compress.pl --level 3 --compressor zstd22 --out {OUT}
geco3-4-zs22geco3-compress.pl --level 4 --compressor zstd22 --out {OUT}
geco3-5-zs22geco3-compress.pl --level 5 --compressor zstd22 --out {OUT}
geco3-6-zs22geco3-compress.pl --level 6 --compressor zstd22 --out {OUT}
geco3-7-zs22geco3-compress.pl --level 7 --compressor zstd22 --out {OUT}
geco3-8-zs22geco3-compress.pl --level 8 --compressor zstd22 --out {OUT}
geco3-9-zs22geco3-compress.pl --level 9 --compressor zstd22 --out {OUT}
geco3-10-zs22geco3-compress.pl --level 10 --compressor zstd22 --out {OUT}
geco3-11-zs22geco3-compress.pl --level 11 --compressor zstd22 --out {OUT}
geco3-12-zs22geco3-compress.pl --level 12 --compressor zstd22 --out {OUT}
geco3-13-zs22geco3-compress.pl --level 13 --compressor zstd22 --out {OUT}
geco3-14-zs22geco3-compress.pl --level 14 --compressor zstd22 --out {OUT}
geco3-15-zs22geco3-compress.pl --level 15 --compressor zstd22 --out {OUT}
geco3-16-zs22geco3-compress.pl --level 16 --compressor zstd22 --out {OUT}
Decompression
geco3-*geco3-decompress.pl --in '{IN}'
Compression, wrapper only
wrap-geco3geco3-compress.pl --level 1 --compressor zstd1 --out {OUT} --wrapper-only
Decompression, wrapper only
wrap-geco3geco3-decompress.pl --in '{IN}' --wrapper-only

gtz

Compression
gtz-1-1tgtz-compress.pl --out {OUT} --level 1 --threads 1
gtz-9-1tgtz-compress.pl --out {OUT} --level 9 --threads 1
gtz-1-4tgtz-compress.pl --out {OUT} --level 1 --threads 4
gtz-9-4tgtz-compress.pl --out {OUT} --level 9 --threads 4
Decompression
gtz-*-1tgtz-decompress.pl --in '{IN}' --threads 1
gtz-*-4tgtz-decompress.pl --in '{IN}' --threads 4
Compression, wrapper only
wrap-gtzgtz-compress.pl --out {OUT} --level 1 --threads 1 --wrapper-only
Decompression, wrapper only
wrap-gtzgtz-decompress.pl --in '{IN}' --threads 1 --wrapper-only

gzip

Compression
gzip-1gzip -c1 >{OUT}
gzip-2gzip -c2 >{OUT}
gzip-3gzip -c3 >{OUT}
gzip-4gzip -c4 >{OUT}
gzip-5gzip -c5 >{OUT}
gzip-6gzip -c6 >{OUT}
gzip-7gzip -c7 >{OUT}
gzip-8gzip -c8 >{OUT}
gzip-9gzip -c9 >{OUT}
Decompression
gzip -dc '{IN}'

harc

DNA compression
harc-1tharc-compress.pl --out {OUT} --threads 1
harc-4tharc-compress.pl --out {OUT} --threads 4
RNA compression
harc-1tharc-compress.pl --out {OUT} --threads 1 --rna
harc-4tharc-compress.pl --out {OUT} --threads 4 --rna
DNA decompression
harc-1tharc-decompress.pl --in '{IN}' --threads 1
harc-4tharc-decompress.pl --in '{IN}' --threads 4
RNA decompression
harc-1tharc-decompress.pl --in '{IN}' --threads 1 --rna
harc-4tharc-decompress.pl --in '{IN}' --threads 4 --rna
DNA compression, wrapper only
wrap-harcharc-compress.pl --out {OUT} --threads 1 --wrapper-only
RNA compression, wrapper only
wrap-harcharc-compress.pl --out {OUT} --threads 1 --rna --wrapper-only
DNA decompression, wrapper only
wrap-harcharc-decompress.pl --in '{IN}' --threads 1 --wrapper-only
RNA decompression, wrapper only
wrap-harcharc-decompress.pl --in '{IN}' --threads 1 --rna --wrapper-only

jarvis

Compression
jarvis-1jarvis-compress.pl --level 1 --out {OUT}
jarvis-2jarvis-compress.pl --level 2 --out {OUT}
jarvis-3jarvis-compress.pl --level 3 --out {OUT}
jarvis-4jarvis-compress.pl --level 4 --out {OUT}
jarvis-5jarvis-compress.pl --level 5 --out {OUT}
jarvis-6jarvis-compress.pl --level 6 --out {OUT}
jarvis-7jarvis-compress.pl --level 7 --out {OUT}
jarvis-8jarvis-compress.pl --level 8 --out {OUT}
jarvis-9jarvis-compress.pl --level 9 --out {OUT}
jarvis-10jarvis-compress.pl --level 10 --out {OUT}
jarvis-11jarvis-compress.pl --level 11 --out {OUT}
jarvis-12jarvis-compress.pl --level 12 --out {OUT}
Decompression
jarvis-*jarvis-decompress.pl --in '{IN}'
Compression, wrapper only
wrap-jarvisjarvis-compress.pl --level 1 --out {OUT} --wrapper-only
Decompression, wrapper only
wrap-jarvisjarvis-decompress.pl --in '{IN}' --wrapper-only

kic

DNA compression
kic-0kic-compress.pl --out {OUT} --mode 0
kic-1kic-compress.pl --out {OUT} --mode 1
kic-2-8kic-compress.pl --out {OUT} --mode 2 --level 8
RNA compression
kic-0kic-compress.pl --out {OUT} --mode 0 --rna
kic-1kic-compress.pl --out {OUT} --mode 1 --rna
kic-2-8kic-compress.pl --out {OUT} --mode 2 --level 8 --rna
DNA decompression
kic-*kic-decompress.pl --in '{IN}'
RNA decompression
kic-*kic-decompress.pl --in '{IN}' --rna
DNA compression, wrapper only
wrap-kickic-compress.pl --out {OUT} --mode 0 --wrapper-only
RNA compression, wrapper only
wrap-kickic-compress.pl --out {OUT} --mode 0 --rna --wrapper-only
DNA decompression, wrapper only
wrap-kickic-decompress.pl --in '{IN}' --wrapper-only
RNA decompression, wrapper only
wrap-kickic-decompress.pl --in '{IN}' --rna --wrapper-only

leon

DNA compression
leon-12leon-compress.pl --out {OUT} --level 12
leon-13leon-compress.pl --out {OUT} --level 13
leon-14leon-compress.pl --out {OUT} --level 14
leon-15leon-compress.pl --out {OUT} --level 15
leon-16leon-compress.pl --out {OUT} --level 16
leon-17leon-compress.pl --out {OUT} --level 17
leon-18leon-compress.pl --out {OUT} --level 18
leon-19leon-compress.pl --out {OUT} --level 19
leon-20leon-compress.pl --out {OUT} --level 20
leon-21leon-compress.pl --out {OUT} --level 21
leon-22leon-compress.pl --out {OUT} --level 22
leon-23leon-compress.pl --out {OUT} --level 23
leon-24leon-compress.pl --out {OUT} --level 24
leon-25leon-compress.pl --out {OUT} --level 25
leon-26leon-compress.pl --out {OUT} --level 26
leon-27leon-compress.pl --out {OUT} --level 27
leon-28leon-compress.pl --out {OUT} --level 28
leon-29leon-compress.pl --out {OUT} --level 29
leon-30leon-compress.pl --out {OUT} --level 30
leon-31leon-compress.pl --out {OUT} --level 31
RNA compression
leon-12leon-compress.pl --out {OUT} --level 12 --rna
leon-13leon-compress.pl --out {OUT} --level 13 --rna
leon-14leon-compress.pl --out {OUT} --level 14 --rna
leon-15leon-compress.pl --out {OUT} --level 15 --rna
leon-16leon-compress.pl --out {OUT} --level 16 --rna
leon-17leon-compress.pl --out {OUT} --level 17 --rna
leon-18leon-compress.pl --out {OUT} --level 18 --rna
leon-19leon-compress.pl --out {OUT} --level 19 --rna
leon-20leon-compress.pl --out {OUT} --level 20 --rna
leon-21leon-compress.pl --out {OUT} --level 21 --rna
leon-22leon-compress.pl --out {OUT} --level 22 --rna
leon-23leon-compress.pl --out {OUT} --level 23 --rna
leon-24leon-compress.pl --out {OUT} --level 24 --rna
leon-25leon-compress.pl --out {OUT} --level 25 --rna
leon-26leon-compress.pl --out {OUT} --level 26 --rna
leon-27leon-compress.pl --out {OUT} --level 27 --rna
leon-28leon-compress.pl --out {OUT} --level 28 --rna
leon-29leon-compress.pl --out {OUT} --level 29 --rna
leon-30leon-compress.pl --out {OUT} --level 30 --rna
leon-31leon-compress.pl --out {OUT} --level 31 --rna
DNA decompression
leon-*leon-decompress.pl --in '{IN}'
RNA decompression
leon-*leon-decompress.pl --in '{IN}' --rna
DNA compression, wrapper only
wrap-leonleon-compress.pl --out {OUT} --level 12 --wrapper-only
RNA compression, wrapper only
wrap-leonleon-compress.pl --out {OUT} --level 12 --rna --wrapper-only
DNA decompression, wrapper only
wrap-leonleon-decompress.pl --in '{IN}' --wrapper-only
RNA decompression, wrapper only
wrap-leonleon-decompress.pl --in '{IN}' --rna --wrapper-only

lfastqc

DNA compression
lfastqclfastqc-compress.pl --out {OUT}
RNA compression
lfastqclfastqc-compress.pl --out {OUT} --rna
DNA decompression
lfastqclfastqc-decompress.pl --in '{IN}'
RNA decompression
lfastqclfastqc-decompress.pl --in '{IN}' --rna
DNA compression, wrapper only
wrap-lfastqclfastqc-compress.pl --out {OUT} --wrapper-only
RNA compression, wrapper only
wrap-lfastqclfastqc-compress.pl --out {OUT} --rna --wrapper-only
DNA decompression, wrapper only
wrap-lfastqclfastqc-decompress.pl --in '{IN}' --wrapper-only
RNA decompression, wrapper only
wrap-lfastqclfastqc-decompress.pl --in '{IN}' --rna --wrapper-only

lfqc

Compression
lfqclfqc-compress.pl --out {OUT} --read-length 4000
Dompression
lfqclfqc-decompress.pl --in '{IN}'
Compression, wrapper only
lfqclfqc-compress.pl --out {OUT} --read-length 4000 --wrapper-only
Dompression, wrapper only
lfqclfqc-decompress.pl --in '{IN}' --wrapper-only

lizard

Compression
lizard-10lizard -10 - {OUT} >/dev/null 2>&1
lizard-11lizard -11 - {OUT} >/dev/null 2>&1
lizard-12lizard -12 - {OUT} >/dev/null 2>&1
lizard-13lizard -13 - {OUT} >/dev/null 2>&1
lizard-14lizard -14 - {OUT} >/dev/null 2>&1
lizard-15lizard -15 - {OUT} >/dev/null 2>&1
lizard-16lizard -16 - {OUT} >/dev/null 2>&1
lizard-17lizard -17 - {OUT} >/dev/null 2>&1
lizard-18lizard -18 - {OUT} >/dev/null 2>&1
lizard-19lizard -19 - {OUT} >/dev/null 2>&1
lizard-20lizard -20 - {OUT} >/dev/null 2>&1
lizard-21lizard -21 - {OUT} >/dev/null 2>&1
lizard-22lizard -22 - {OUT} >/dev/null 2>&1
lizard-23lizard -23 - {OUT} >/dev/null 2>&1
lizard-24lizard -24 - {OUT} >/dev/null 2>&1
lizard-25lizard -25 - {OUT} >/dev/null 2>&1
lizard-26lizard -26 - {OUT} >/dev/null 2>&1
lizard-27lizard -27 - {OUT} >/dev/null 2>&1
lizard-28lizard -28 - {OUT} >/dev/null 2>&1
lizard-29lizard -29 - {OUT} >/dev/null 2>&1
lizard-30lizard -30 - {OUT} >/dev/null 2>&1
lizard-31lizard -31 - {OUT} >/dev/null 2>&1
lizard-32lizard -32 - {OUT} >/dev/null 2>&1
lizard-33lizard -33 - {OUT} >/dev/null 2>&1
lizard-34lizard -34 - {OUT} >/dev/null 2>&1
lizard-35lizard -35 - {OUT} >/dev/null 2>&1
lizard-36lizard -36 - {OUT} >/dev/null 2>&1
lizard-37lizard -37 - {OUT} >/dev/null 2>&1
lizard-38lizard -38 - {OUT} >/dev/null 2>&1
lizard-39lizard -39 - {OUT} >/dev/null 2>&1
lizard-40lizard -40 - {OUT} >/dev/null 2>&1
lizard-41lizard -41 - {OUT} >/dev/null 2>&1
lizard-42lizard -42 - {OUT} >/dev/null 2>&1
lizard-43lizard -43 - {OUT} >/dev/null 2>&1
lizard-44lizard -44 - {OUT} >/dev/null 2>&1
lizard-45lizard -45 - {OUT} >/dev/null 2>&1
lizard-46lizard -46 - {OUT} >/dev/null 2>&1
lizard-47lizard -47 - {OUT} >/dev/null 2>&1
lizard-48lizard -48 - {OUT} >/dev/null 2>&1
lizard-49lizard -49 - {OUT} >/dev/null 2>&1
Decompression
lizard -dc '{IN}'

lz4

Compression
lz4-1lz4 -1 -c >{OUT}
lz4-2lz4 -2 -c >{OUT}
lz4-3lz4 -3 -c >{OUT}
lz4-4lz4 -4 -c >{OUT}
lz4-5lz4 -5 -c >{OUT}
lz4-6lz4 -6 -c >{OUT}
lz4-7lz4 -7 -c >{OUT}
lz4-8lz4 -8 -c >{OUT}
lz4-9lz4 -9 -c >{OUT}
Decompression
lz4 -dc '{IN}'

lzop

Compression
lzop-1lzop -1 -c >{OUT}
lzop-9lzop -9 -c >{OUT}
Decompression
lzop -dc '{IN}'

lzturbo

Compression
lzturbo-10-1tlzturbo_static -10 -p0 -o >{OUT}
lzturbo-11-1tlzturbo_static -11 -p0 -o >{OUT}
lzturbo-12-1tlzturbo_static -12 -p0 -o >{OUT}
lzturbo-19-1tlzturbo_static -19 -p0 -o >{OUT}
lzturbo-20-1tlzturbo_static -20 -p0 -o >{OUT}
lzturbo-21-1tlzturbo_static -21 -p0 -o >{OUT}
lzturbo-22-1tlzturbo_static -22 -p0 -o >{OUT}
lzturbo-29-1tlzturbo_static -29 -p0 -o >{OUT}
lzturbo-30-1tlzturbo_static -30 -p0 -o >{OUT}
lzturbo-31-1tlzturbo_static -31 -p0 -o >{OUT}
lzturbo-32-1tlzturbo_static -32 -p0 -o >{OUT}
lzturbo-39-1tlzturbo_static -39 -p0 -o >{OUT}
lzturbo-49-1tlzturbo_static -49 -p0 -o >{OUT}
lzturbo-10-4tlzturbo_static -10 -p4 -o >{OUT}
lzturbo-11-4tlzturbo_static -11 -p4 -o >{OUT}
lzturbo-12-4tlzturbo_static -12 -p4 -o >{OUT}
lzturbo-19-4tlzturbo_static -19 -p4 -o >{OUT}
lzturbo-20-4tlzturbo_static -20 -p4 -o >{OUT}
lzturbo-21-4tlzturbo_static -21 -p4 -o >{OUT}
lzturbo-22-4tlzturbo_static -22 -p4 -o >{OUT}
lzturbo-29-4tlzturbo_static -29 -p4 -o >{OUT}
lzturbo-30-4tlzturbo_static -30 -p4 -o >{OUT}
lzturbo-31-4tlzturbo_static -31 -p4 -o >{OUT}
lzturbo-32-4tlzturbo_static -32 -p4 -o >{OUT}
lzturbo-39-4tlzturbo_static -39 -p4 -o >{OUT}
lzturbo-49-4tlzturbo_static -49 -p4 -o >{OUT}
Decompression
lzturbo-static-decompress.pl '{IN}'

mfc

DNA compression
mfc-1mfc-compress.pl --out {OUT} --level 1
mfc-2mfc-compress.pl --out {OUT} --level 2
mfc-3mfc-compress.pl --out {OUT} --level 3
RNA compression
mfc-1mfc-compress.pl --out {OUT} --rna --level 1
mfc-2mfc-compress.pl --out {OUT} --rna --level 2
mfc-3mfc-compress.pl --out {OUT} --rna --level 3
DNA decompression
mfc-decompress.pl --in '{IN}'
RNA decompression
mfc-decompress.pl --in '{IN}' --rna

minicom

DNA compression
minicom-1tminicom-compress.pl --out {OUT} --read-length 250 --threads 1
minicom-4tminicom-compress.pl --out {OUT} --read-length 250 --threads 4
DNA decompression
minicom-1tminicom-decompress.pl --in '{IN}' --threads 1
minicom-4tminicom-decompress.pl --in '{IN}' --threads 4
DNA compression, wrapper only
wrap-minicomminicom-compress.pl --out {OUT} --read-length 250 --threads 1 --wrapper-only
DNA decompression, wrapper only
wrap-minicomminicom-decompress.pl --in '{IN}' --threads 1 --wrapper-only

naf

DNA compression
naf-1ennaf --fasta --dna --name {NAME} -1 -o {OUT}
naf-2ennaf --fasta --dna --name {NAME} -2 -o {OUT}
naf-3ennaf --fasta --dna --name {NAME} -3 -o {OUT}
naf-4ennaf --fasta --dna --name {NAME} -4 -o {OUT}
naf-5ennaf --fasta --dna --name {NAME} -5 -o {OUT}
naf-6ennaf --fasta --dna --name {NAME} -6 -o {OUT}
naf-7ennaf --fasta --dna --name {NAME} -7 -o {OUT}
naf-8ennaf --fasta --dna --name {NAME} -8 -o {OUT}
naf-9ennaf --fasta --dna --name {NAME} -9 -o {OUT}
naf-10ennaf --fasta --dna --name {NAME} -10 -o {OUT}
naf-11ennaf --fasta --dna --name {NAME} -11 -o {OUT}
naf-12ennaf --fasta --dna --name {NAME} -12 -o {OUT}
naf-13ennaf --fasta --dna --name {NAME} -13 -o {OUT}
naf-14ennaf --fasta --dna --name {NAME} -14 -o {OUT}
naf-15ennaf --fasta --dna --name {NAME} -15 -o {OUT}
naf-16ennaf --fasta --dna --name {NAME} -16 -o {OUT}
naf-17ennaf --fasta --dna --name {NAME} -17 -o {OUT}
naf-18ennaf --fasta --dna --name {NAME} -18 -o {OUT}
naf-19ennaf --fasta --dna --name {NAME} -19 -o {OUT}
naf-20ennaf --fasta --dna --name {NAME} -20 -o {OUT}
naf-21ennaf --fasta --dna --name {NAME} -21 -o {OUT}
naf-22ennaf --fasta --dna --name {NAME} -22 -o {OUT}
naf-22-31ennaf --fasta --dna --name {NAME} -22 --long 31 -o {OUT}
naf-text-1ennaf --fasta --text --name {NAME} -1 -o {OUT}
naf-text-2ennaf --fasta --text --name {NAME} -2 -o {OUT}
naf-text-3ennaf --fasta --text --name {NAME} -3 -o {OUT}
naf-text-4ennaf --fasta --text --name {NAME} -4 -o {OUT}
naf-text-5ennaf --fasta --text --name {NAME} -5 -o {OUT}
naf-text-6ennaf --fasta --text --name {NAME} -6 -o {OUT}
naf-text-7ennaf --fasta --text --name {NAME} -7 -o {OUT}
naf-text-8ennaf --fasta --text --name {NAME} -8 -o {OUT}
naf-text-9ennaf --fasta --text --name {NAME} -9 -o {OUT}
naf-text-10ennaf --fasta --text --name {NAME} -10 -o {OUT}
naf-text-11ennaf --fasta --text --name {NAME} -11 -o {OUT}
naf-text-12ennaf --fasta --text --name {NAME} -12 -o {OUT}
naf-text-13ennaf --fasta --text --name {NAME} -13 -o {OUT}
naf-text-14ennaf --fasta --text --name {NAME} -14 -o {OUT}
naf-text-15ennaf --fasta --text --name {NAME} -15 -o {OUT}
naf-text-16ennaf --fasta --text --name {NAME} -16 -o {OUT}
naf-text-17ennaf --fasta --text --name {NAME} -17 -o {OUT}
naf-text-18ennaf --fasta --text --name {NAME} -18 -o {OUT}
naf-text-19ennaf --fasta --text --name {NAME} -19 -o {OUT}
naf-text-20ennaf --fasta --text --name {NAME} -20 -o {OUT}
naf-text-21ennaf --fasta --text --name {NAME} -21 -o {OUT}
naf-text-22ennaf --fasta --text --name {NAME} -22 -o {OUT}
naf-text-22-31ennaf --fasta --text --name {NAME} -22 --long 31 -o {OUT}
RNA compression
naf-1ennaf --fasta --rna --name {NAME} -1 -o {OUT}
naf-2ennaf --fasta --rna --name {NAME} -2 -o {OUT}
naf-3ennaf --fasta --rna --name {NAME} -3 -o {OUT}
naf-4ennaf --fasta --rna --name {NAME} -4 -o {OUT}
naf-5ennaf --fasta --rna --name {NAME} -5 -o {OUT}
naf-6ennaf --fasta --rna --name {NAME} -6 -o {OUT}
naf-7ennaf --fasta --rna --name {NAME} -7 -o {OUT}
naf-8ennaf --fasta --rna --name {NAME} -8 -o {OUT}
naf-9ennaf --fasta --rna --name {NAME} -9 -o {OUT}
naf-10ennaf --fasta --rna --name {NAME} -10 -o {OUT}
naf-11ennaf --fasta --rna --name {NAME} -11 -o {OUT}
naf-12ennaf --fasta --rna --name {NAME} -12 -o {OUT}
naf-13ennaf --fasta --rna --name {NAME} -13 -o {OUT}
naf-14ennaf --fasta --rna --name {NAME} -14 -o {OUT}
naf-15ennaf --fasta --rna --name {NAME} -15 -o {OUT}
naf-16ennaf --fasta --rna --name {NAME} -16 -o {OUT}
naf-17ennaf --fasta --rna --name {NAME} -17 -o {OUT}
naf-18ennaf --fasta --rna --name {NAME} -18 -o {OUT}
naf-19ennaf --fasta --rna --name {NAME} -19 -o {OUT}
naf-20ennaf --fasta --rna --name {NAME} -20 -o {OUT}
naf-21ennaf --fasta --rna --name {NAME} -21 -o {OUT}
naf-22-31ennaf --fasta --rna --name {NAME} -22 --long 31 -o {OUT}
naf-text-1ennaf --fasta --text --name {NAME} -1 -o {OUT}
naf-text-2ennaf --fasta --text --name {NAME} -2 -o {OUT}
naf-text-3ennaf --fasta --text --name {NAME} -3 -o {OUT}
naf-text-4ennaf --fasta --text --name {NAME} -4 -o {OUT}
naf-text-5ennaf --fasta --text --name {NAME} -5 -o {OUT}
naf-text-6ennaf --fasta --text --name {NAME} -6 -o {OUT}
naf-text-7ennaf --fasta --text --name {NAME} -7 -o {OUT}
naf-text-8ennaf --fasta --text --name {NAME} -8 -o {OUT}
naf-text-9ennaf --fasta --text --name {NAME} -9 -o {OUT}
naf-text-10ennaf --fasta --text --name {NAME} -10 -o {OUT}
naf-text-11ennaf --fasta --text --name {NAME} -11 -o {OUT}
naf-text-12ennaf --fasta --text --name {NAME} -12 -o {OUT}
naf-text-13ennaf --fasta --text --name {NAME} -13 -o {OUT}
naf-text-14ennaf --fasta --text --name {NAME} -14 -o {OUT}
naf-text-15ennaf --fasta --text --name {NAME} -15 -o {OUT}
naf-text-16ennaf --fasta --text --name {NAME} -16 -o {OUT}
naf-text-17ennaf --fasta --text --name {NAME} -17 -o {OUT}
naf-text-18ennaf --fasta --text --name {NAME} -18 -o {OUT}
naf-text-19ennaf --fasta --text --name {NAME} -19 -o {OUT}
naf-text-20ennaf --fasta --text --name {NAME} -20 -o {OUT}
naf-text-21ennaf --fasta --text --name {NAME} -21 -o {OUT}
naf-text-22-31ennaf --fasta --text --name {NAME} -22 --long 31 -o {OUT}
Protein compression
naf-1ennaf --fasta --protein --name {NAME} -1 -o {OUT}
naf-2ennaf --fasta --protein --name {NAME} -2 -o {OUT}
naf-3ennaf --fasta --protein --name {NAME} -3 -o {OUT}
naf-4ennaf --fasta --protein --name {NAME} -4 -o {OUT}
naf-5ennaf --fasta --protein --name {NAME} -5 -o {OUT}
naf-6ennaf --fasta --protein --name {NAME} -6 -o {OUT}
naf-7ennaf --fasta --protein --name {NAME} -7 -o {OUT}
naf-8ennaf --fasta --protein --name {NAME} -8 -o {OUT}
naf-9ennaf --fasta --protein --name {NAME} -9 -o {OUT}
naf-10ennaf --fasta --protein --name {NAME} -10 -o {OUT}
naf-11ennaf --fasta --protein --name {NAME} -11 -o {OUT}
naf-12ennaf --fasta --protein --name {NAME} -12 -o {OUT}
naf-13ennaf --fasta --protein --name {NAME} -13 -o {OUT}
naf-14ennaf --fasta --protein --name {NAME} -14 -o {OUT}
naf-15ennaf --fasta --protein --name {NAME} -15 -o {OUT}
naf-16ennaf --fasta --protein --name {NAME} -16 -o {OUT}
naf-17ennaf --fasta --protein --name {NAME} -17 -o {OUT}
naf-18ennaf --fasta --protein --name {NAME} -18 -o {OUT}
naf-19ennaf --fasta --protein --name {NAME} -19 -o {OUT}
naf-20ennaf --fasta --protein --name {NAME} -20 -o {OUT}
naf-21ennaf --fasta --protein --name {NAME} -21 -o {OUT}
naf-22ennaf --fasta --protein --name {NAME} -22 -o {OUT}
naf-22-31ennaf --fasta --protein --name {NAME} -22 --long 31 -o {OUT}
Decompression
unnaf '{IN}'

nakamichi

Compression
nakamichinakamichi-compress.pl --out {OUT} --hashsize 28 --treesize 81000 --treetype i
Decompression
nakamichinakamichi '{IN}'

nuht

DNA compression
nuhtnuht-compress.pl --out {OUT}
RNA compression
nuhtnuht-compress.pl --out {OUT} --rna
DNA decompression
nuhtnuht-decompress.pl --in '{IN}'
RNA decompression
nuhtnuht-decompress.pl --in '{IN}' --rna
DNA compression, wrapper only
wrap-nuhtnuht-compress.pl --out {OUT} --wrapper-only
RNA compression, wrapper only
wrap-nuhtnuht-compress.pl --out {OUT} --rna --wrapper-only
DNA decompression, wrapper only
wrap-nuhtnuht-decompress.pl --in '{IN}' --wrapper-only
RNA decompression, wrapper only
wrap-nuhtnuht-decompress.pl --in '{IN}' --rna --wrapper-only

pbzip2

Compression
pbzip2-1-1tpbzip2 -1 -c -z -p1 >{OUT}
pbzip2-2-1tpbzip2 -2 -c -z -p1 >{OUT}
pbzip2-3-1tpbzip2 -3 -c -z -p1 >{OUT}
pbzip2-4-1tpbzip2 -4 -c -z -p1 >{OUT}
pbzip2-5-1tpbzip2 -5 -c -z -p1 >{OUT}
pbzip2-6-1tpbzip2 -6 -c -z -p1 >{OUT}
pbzip2-7-1tpbzip2 -7 -c -z -p1 >{OUT}
pbzip2-8-1tpbzip2 -8 -c -z -p1 >{OUT}
pbzip2-9-1tpbzip2 -9 -c -z -p1 >{OUT}
pbzip2-1-4tpbzip2 -1 -c -z -p4 >{OUT}
pbzip2-2-4tpbzip2 -2 -c -z -p4 >{OUT}
pbzip2-3-4tpbzip2 -3 -c -z -p4 >{OUT}
pbzip2-4-4tpbzip2 -4 -c -z -p4 >{OUT}
pbzip2-5-4tpbzip2 -5 -c -z -p4 >{OUT}
pbzip2-6-4tpbzip2 -6 -c -z -p4 >{OUT}
pbzip2-7-4tpbzip2 -7 -c -z -p4 >{OUT}
pbzip2-8-4tpbzip2 -8 -c -z -p4 >{OUT}
pbzip2-9-4tpbzip2 -9 -c -z -p4 >{OUT}
Decompression
pbzip2 -dc '{IN}'

pigz

Compression
pigz-1-1tpigz -p 1 -c -1 >{OUT}
pigz-2-1tpigz -p 1 -c -2 >{OUT}
pigz-3-1tpigz -p 1 -c -3 >{OUT}
pigz-4-1tpigz -p 1 -c -4 >{OUT}
pigz-5-1tpigz -p 1 -c -5 >{OUT}
pigz-6-1tpigz -p 1 -c -6 >{OUT}
pigz-7-1tpigz -p 1 -c -7 >{OUT}
pigz-8-1tpigz -p 1 -c -8 >{OUT}
pigz-9-1tpigz -p 1 -c -9 >{OUT}
pigz-11-1tpigz -p 1 -c -11 >{OUT}
pigz-1-4tpigz -p 4 -c -1 >{OUT}
pigz-2-4tpigz -p 4 -c -2 >{OUT}
pigz-3-4tpigz -p 4 -c -3 >{OUT}
pigz-4-4tpigz -p 4 -c -4 >{OUT}
pigz-5-4tpigz -p 4 -c -5 >{OUT}
pigz-6-4tpigz -p 4 -c -6 >{OUT}
pigz-7-4tpigz -p 4 -c -7 >{OUT}
pigz-8-4tpigz -p 4 -c -8 >{OUT}
pigz-9-4tpigz -p 4 -c -9 >{OUT}
pigz-11-4tpigz -p 4 -c -11 >{OUT}
Decompression
pigz -dc '{IN}'

pfish

DNA compression
pfishpfish-compress.pl --out {OUT}
RNA compression
pfishpfish-compress.pl --out {OUT} --rna
DNA decompression
pfishpfish-decompress.pl --in '{IN}'
RNA decompression
pfishpfish-decompress.pl --in '{IN}' --rna
DNA compression, wrapper only
wrap-pfishpfish-compress.pl --out {OUT} --wrapper-only
RNA compression, wrapper only
wrap-pfishpfish-compress.pl --out {OUT} --rna --wrapper-only
DNA decompression, wrapper only
wrap-pfishpfish-decompress.pl --in '{IN}' --wrapper-only
RNA decompression, wrapper only
wrap-pfishpfish-decompress.pl --in '{IN}' --rna --wrapper-only

quip

DNA compression
quipquip-compress.pl --out {OUT}
RNA compression
quipquip-compress.pl --out {OUT} --rna
DNA decompression
quipquip-decompress.pl --in '{IN}'
RNA decompression
quipquip-decompress.pl --in '{IN}' --rna
DNA compression, wrapper only
wrap-quipquip-compress.pl --out {OUT} --wrapper-only
RNA compression, wrapper only
wrap-quipquip-compress.pl --out {OUT} --rna --wrapper-only
DNA decompression, wrapper only
wrap-quipquip-decompress.pl --in '{IN}' --wrapper-only
RNA decompression, wrapper only
wrap-quipquip-decompress.pl --in '{IN}' --rna --wrapper-only

snzip

Compression
snzip -c >{OUT}
Decompression
snzip -dc '{IN}'

spring

DNA compression
spring-l-1tspring-long-compress.pl --out {OUT} --threads 1
spring-l-4tspring-long-compress.pl --out {OUT} --threads 4
spring-s-1tspring-short-compress.pl --out {OUT} --read-length 500 --threads 1
spring-s-4tspring-short-compress.pl --out {OUT} --read-length 500 --threads 4
RNA compression
spring-l-1tspring-long-compress.pl --out {OUT} --threads 1
spring-l-4tspring-long-compress.pl --out {OUT} --threads 4
spring-s-1tspring-short-compress.pl --out {OUT} --read-length 500 --threads 1 --rna
spring-s-4tspring-short-compress.pl --out {OUT} --read-length 500 --threads 4 --rna
DNA decompression
spring-l-1tspring-long-decompress.pl --in '{IN}' --threads 1
spring-l-4tspring-long-decompress.pl --in '{IN}' --threads 4
spring-s-1tspring-short-decompress.pl --in '{IN}' --threads 1
spring-s-4tspring-short-decompress.pl --in '{IN}' --threads 4
RNA decompression
spring-l-1tspring-long-decompress.pl --in '{IN}' --threads 1
spring-l-4tspring-long-decompress.pl --in '{IN}' --threads 4
spring-s-1tspring-short-decompress.pl --in '{IN}' --threads 1 --rna
spring-s-4tspring-short-decompress.pl --in '{IN}' --threads 4 --rna
DNA compression, wrapper only
wrap-spring-lspring-long-compress.pl --out {OUT} --threads 1 --wrapper-only
wrap-spring-sspring-short-compress.pl --out {OUT} --read-length 500 --threads 1 --wrapper-only
RNA compression, wrapper only
wrap-spring-lspring-long-compress.pl --out {OUT} --threads 1 --wrapper-only
wrap-spring-sspring-short-compress.pl --out {OUT} --read-length 500 --threads 1 --rna --wrapper-only
DNA decompression, wrapper only
wrap-spring-lspring-long-decompress.pl --in '{IN}' --threads 1 --wrapper-only
wrap-spring-sspring-short-decompress.pl --in '{IN}' --threads 1 --wrapper-only
RNA decompression, wrapper only
wrap-spring-lspring-long-decompress.pl --in '{IN}' --threads 1 --wrapper-only
wrap-spring-sspring-short-decompress.pl --in '{IN}' --threads 1 --rna --wrapper-only

uht

Compression
uhtuht-compress.pl --out {OUT}
Decompression
uhtuht-decompress.pl --in '{IN}'
Compression, wrapper only
wrap-uhtuht-compress.pl --out {OUT} --wrapper-only
Decompression, wrapper only
wrap-uhtuht-decompress.pl --in '{IN}' --wrapper-only

xm

Compression
xm-9-0.15-zs1xm-compress.pl --out {OUT} --hashSize 9 --context 15 --limit 200 --threshold 0.15 --chance 20 --compressor zstd1
xm-9-0.50-zs1xm-compress.pl --out {OUT} --hashSize 9 --context 15 --limit 200 --threshold 0.50 --chance 20 --compressor zstd1
xm-10-0.15-zs1xm-compress.pl --out {OUT} --hashSize 10 --context 15 --limit 200 --threshold 0.15 --chance 20 --compressor zstd1
xm-10-0.50-zs1xm-compress.pl --out {OUT} --hashSize 10 --context 15 --limit 200 --threshold 0.50 --chance 20 --compressor zstd1
xm-11-0.15-zs1xm-compress.pl --out {OUT} --hashSize 11 --context 15 --limit 200 --threshold 0.15 --chance 20 --compressor zstd1
xm-11-0.50-zs1xm-compress.pl --out {OUT} --hashSize 11 --context 15 --limit 200 --threshold 0.50 --chance 20 --compressor zstd1
xm-12-0.15-zs1xm-compress.pl --out {OUT} --hashSize 12 --context 15 --limit 200 --threshold 0.15 --chance 20 --compressor zstd1
xm-12-0.50-zs1xm-compress.pl --out {OUT} --hashSize 12 --context 15 --limit 200 --threshold 0.50 --chance 20 --compressor zstd1
xm-13-0.15-zs1xm-compress.pl --out {OUT} --hashSize 13 --context 15 --limit 200 --threshold 0.15 --chance 20 --compressor zstd1
xm-13-0.50-zs1xm-compress.pl --out {OUT} --hashSize 13 --context 15 --limit 200 --threshold 0.50 --chance 20 --compressor zstd1
xm-9-0.15-zs22xm-compress.pl --out {OUT} --hashSize 9 --context 15 --limit 200 --threshold 0.15 --chance 20 --compressor zstd22
xm-9-0.50-zs22xm-compress.pl --out {OUT} --hashSize 9 --context 15 --limit 200 --threshold 0.50 --chance 20 --compressor zstd22
xm-10-0.15-zs22xm-compress.pl --out {OUT} --hashSize 10 --context 15 --limit 200 --threshold 0.15 --chance 20 --compressor zstd22
xm-10-0.50-zs22xm-compress.pl --out {OUT} --hashSize 10 --context 15 --limit 200 --threshold 0.50 --chance 20 --compressor zstd22
xm-11-0.15-zs22xm-compress.pl --out {OUT} --hashSize 11 --context 15 --limit 200 --threshold 0.15 --chance 20 --compressor zstd22
xm-11-0.50-zs22xm-compress.pl --out {OUT} --hashSize 11 --context 15 --limit 200 --threshold 0.50 --chance 20 --compressor zstd22
xm-12-0.15-zs22xm-compress.pl --out {OUT} --hashSize 12 --context 15 --limit 200 --threshold 0.15 --chance 20 --compressor zstd22
xm-12-0.50-zs22xm-compress.pl --out {OUT} --hashSize 12 --context 15 --limit 200 --threshold 0.50 --chance 20 --compressor zstd22
xm-13-0.15-zs22xm-compress.pl --out {OUT} --hashSize 13 --context 15 --limit 200 --threshold 0.15 --chance 20 --compressor zstd22
xm-13-0.50-zs22xm-compress.pl --out {OUT} --hashSize 13 --context 15 --limit 200 --threshold 0.50 --chance 20 --compressor zstd22
Decompression
xm-*xm-decompress.pl --in '{IN}'
Compression, wrapper only
wrap-xmxm-compress.pl --out {OUT} --hashSize 9 --context 15 --limit 200 --threshold 0.15 --chance 20 --compressor zstd1 --wrapper-only
Decompression, wrapper only
wrap-xmxm-decompress.pl --in '{IN}' --wrapper-only

xz

Compression
xz-0xz -zkc0 >{OUT}
xz-1xz -zkc1 >{OUT}
xz-2xz -zkc2 >{OUT}
xz-3xz -zkc3 >{OUT}
xz-4xz -zkc4 >{OUT}
xz-5xz -zkc5 >{OUT}
xz-6xz -zkc6 >{OUT}
xz-7xz -zkc7 >{OUT}
xz-8xz -zkc8 >{OUT}
xz-9xz -zkc9 >{OUT}
xz-e0xz -zkce0 >{OUT}
xz-e1xz -zkce1 >{OUT}
xz-e2xz -zkce2 >{OUT}
xz-e3xz -zkce3 >{OUT}
xz-e4xz -zkce4 >{OUT}
xz-e5xz -zkce5 >{OUT}
xz-e6xz -zkce6 >{OUT}
xz-e7xz -zkce7 >{OUT}
xz-e8xz -zkce8 >{OUT}
xz-e9xz -zkce9 >{OUT}
Decompression
xz -dc '{IN}'

zpaq

Compression
zpaq-1-1tzpaq-compress.pl --out {OUT} --level 1 --threads 1
zpaq-2-1tzpaq-compress.pl --out {OUT} --level 2 --threads 1
zpaq-3-1tzpaq-compress.pl --out {OUT} --level 3 --threads 1
zpaq-4-1tzpaq-compress.pl --out {OUT} --level 4 --threads 1
zpaq-5-1tzpaq-compress.pl --out {OUT} --level 5 --threads 1
zpaq-1-4tzpaq-compress.pl --out {OUT} --level 1 --threads 4
zpaq-2-4tzpaq-compress.pl --out {OUT} --level 2 --threads 4
zpaq-3-4tzpaq-compress.pl --out {OUT} --level 3 --threads 4
zpaq-4-4tzpaq-compress.pl --out {OUT} --level 4 --threads 4
zpaq-5-4tzpaq-compress.pl --out {OUT} --level 5 --threads 4
Decompression
zpaq-decompress.pl '{IN}'

zpipe

Compression
zpipe-1zpipe -1 >{OUT}
zpipe-2zpipe -2 >{OUT}
zpipe-3zpipe -3 >{OUT}
Decompression
zpipe -d <'{IN}'

zstd

Compression
zstd-1-1tzstd --single-thread -1 -c >{OUT}
zstd-2-1tzstd --single-thread -2 -c >{OUT}
zstd-3-1tzstd --single-thread -3 -c >{OUT}
zstd-4-1tzstd --single-thread -4 -c >{OUT}
zstd-5-1tzstd --single-thread -5 -c >{OUT}
zstd-6-1tzstd --single-thread -6 -c >{OUT}
zstd-7-1tzstd --single-thread -7 -c >{OUT}
zstd-8-1tzstd --single-thread -8 -c >{OUT}
zstd-9-1tzstd --single-thread -9 -c >{OUT}
zstd-10-1tzstd --single-thread -10 -c >{OUT}
zstd-11-1tzstd --single-thread -11 -c >{OUT}
zstd-12-1tzstd --single-thread -12 -c >{OUT}
zstd-13-1tzstd --single-thread -13 -c >{OUT}
zstd-14-1tzstd --single-thread -14 -c >{OUT}
zstd-15-1tzstd --single-thread -15 -c >{OUT}
zstd-16-1tzstd --single-thread -16 -c >{OUT}
zstd-17-1tzstd --single-thread -17 -c >{OUT}
zstd-18-1tzstd --single-thread -18 -c >{OUT}
zstd-19-1tzstd --single-thread -19 -c >{OUT}
zstd-20-1tzstd --single-thread --ultra -20 -c >{OUT}
zstd-21-1tzstd --single-thread --ultra -21 -c >{OUT}
zstd-22-1tzstd --single-thread --ultra -22 -c >{OUT}
zstd-22-31-1tzstd --single-thread --ultra -22 --long=31 -c >{OUT}
zstd-1-4tzstd -T4 -1 -c >{OUT}
zstd-2-4tzstd -T4 -2 -c >{OUT}
zstd-3-4tzstd -T4 -3 -c >{OUT}
zstd-4-4tzstd -T4 -4 -c >{OUT}
zstd-5-4tzstd -T4 -5 -c >{OUT}
zstd-6-4tzstd -T4 -6 -c >{OUT}
zstd-7-4tzstd -T4 -7 -c >{OUT}
zstd-8-4tzstd -T4 -8 -c >{OUT}
zstd-9-4tzstd -T4 -9 -c >{OUT}
zstd-10-4tzstd -T4 -10 -c >{OUT}
zstd-11-4tzstd -T4 -11 -c >{OUT}
zstd-12-4tzstd -T4 -12 -c >{OUT}
zstd-13-4tzstd -T4 -13 -c >{OUT}
zstd-14-4tzstd -T4 -14 -c >{OUT}
zstd-15-4tzstd -T4 -15 -c >{OUT}
zstd-16-4tzstd -T4 -16 -c >{OUT}
zstd-17-4tzstd -T4 -17 -c >{OUT}
zstd-18-4tzstd -T4 -18 -c >{OUT}
zstd-19-4tzstd -T4 -19 -c >{OUT}
zstd-20-4tzstd -T4 --ultra -20 -c >{OUT}
zstd-21-4tzstd -T4 --ultra -21 -c >{OUT}
zstd-22-4tzstd -T4 --ultra -22 -c >{OUT}
zstd-22-31-4tzstd -T4 --ultra -22 --long=31 -c >{OUT}
Decompression
zstd-*-31-*zstd -dc --long=31 '{IN}' 2>/dev/null
zstdzstd -dc '{IN}' 2>/dev/null
By Contributors, 2019-2022, public domain