A versatile compressor of third generation sequencing reads.
git clone https://github.com/refresh-bio/CoLoRd
cd colord && make
cd bin
INPUT=./../test
# default compression presets (lossy quality, memory priority)
./colord compress-ont ${INPUT}/M.bovis.fastq ont.default # Oxford Nanopore
./colord compress-pbhifi ${INPUT}/D.melanogaster.fastq hifi.default # PacBio HiFi
./colord compress-pbraw ${INPUT}/A.thaliana.fastq clr.default # PacBio CLR/subreads
# print ONT archive information and decompress
./colord info ont.default
./colord decompress ont.default ont.fastq
# compress HiFi reads preserving original quality levels
./colord compress-pbhifi -q org ${INPUT}/D.melanogaster.fastq hifi.lossless
# compress CLR reads with ratio priority using 48 threads
./colord compress-pbraw -p ratio -t 48 ${INPUT}/A.thaliana.fastq clr.ratio
# compress ONT reads w.r.t. reference genome (embed the reference in the archive)
./colord compress-ont -G ${INPUT}/M.bovis-reference.fna -s ${INPUT}/M.bovis.fastq ont.refbased
# decompress the reference-based archive
./colord decompress ont.refbased ont.refbased.fastq
CoLoRd comes with a set of precompiled binaries for Windows, Linux, and OS X. They can be found under Releases tab.
CoLoRd can be also built from the sources distributed as:
- Visual Studio 2019 solution for Windows,
- MAKE project (G++ 8.4 required) for Linux and macOS.
To install G++ under under macOS, one can use Homebrew package manager:
/usr/bin/ruby -e "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/master/install)"
brew install gcc@10
Before running CoLoRd on macOS, the current limit of file descriptors should be increased:
ulimit -n 2048
colord <mode> [options] <input> <archive>
Modes:
compress-ont- compress Oxford Nanopore reads,compress-pbhifi- compress PacBio HiFi reads,compress-pbraw- compress PacBio CLR/subreads.
Positionals:
input- input FASTQ/FASTA path (gzipped or not),output- archive path.
Options:
-h, --help- print help-k, --kmer-len- k-mer length, (15-28, default: auto adjust)-t, --threads- number of threads (default: 12)-p, --priority- compression priority:memory,balanced,ratio(default:memory)-q, --qual- quality compression mode:org- original,none- discard (Q0 for all bases),avg- average over entire file,2-fix,4-fix,5-fix- 2/4/5 bins with fixed representatives,2-avg,4-avg,5-avg- 2/4/5 bins with averages as representatives; default value depends on the mode (4-avgforont,5-avgforpbhifi,noneforpbraw),
-T, --qual-thresholds- quality thresholds:- single value for
2-fix/2-avg(default: 7), - three values for
4-fix/4-avg(default: 7 14 26), - four values for
4-fix/4-avg(default: 7 14 26 93), - not allowed for
avg,organdnonemodes,
- single value for
-D, --qual-values- bin representatives for decompression,- single value for
nonemode (default: 0), - two values for
2-fixmode (default: 1 13), - four values for
4-fixmode (default: 3 10 18 35), - five values for
5-fixmode (default: 3 10 18 35 93), - not allowed for
avg,org,2-avg,4-avgand5-avgmodes,
- single value for
-G, --reference-genome- optional reference genome path (multi-FASTA gzipped or not), it enables reference-based mode which provides better compression ratios,-s, --store-reference- stores the reference genome in the archive, use only with-Gflag,-v, --verbose- verbose mode.
Advanced options (default values may depend on the mode - please run colord --help <mode> to get the details):
-a, --anchor-len- anchor len (default: auto adjust),-L, --Lowest-count- minimal k-mer count,-H, --Highest-count- maximal k-mer count,-f, --filter-modulo- k-mers for which hash(k-mer) mod f != 0 will be filtered out before graph building,-c, --max-candidates- maximal number of reference reads considered as reference,-e, --edit-script-mult- multipier for predicted cost of storing read part as edit script,-r, --max-recurence-level- maximal level of recurence when considering alternative reference reads,--min-to-alt- minimum length of encoding part to consider using alternative read,--min-mmer-frac- if A is set of m-mers in encode read R then read is refused from encoding if |A| < min-mmer-frac * len(R),--min-mmer-force-enc- if A is set of m-mers in encode read R then read is accepted to encoding always if |A| > min-mmer-force-enc * len(R),--max-matches-mult- if the number of matches between encode read R and reference read is r, then read is refused from encoding if r > max-matches-mult * len(R),--fill-factor-filtered-kmers- fill factor of filtered k-mers hash table,--fill-factor-kmers-to-reads- fill factor of k-mers to reads hash table,--min-anchors- if number of anchors common to encode read and reference candidate is lower than minAnchors candidate is refused,-i, --identifierheader compression mode -main/none/org(default:org),-R, --Ref-reads-mode- reference reads mode:all/sparse(default:sparse),-g, --sparse-range- sparse mode range. The propability of reference read acceptance is 1 / pow(id/range_reads, exponent), where range_reads is determined based on the number of symbols, which in turn is determined by the number of trusted unique k-mers (estimated genome length) multiplied by the value of this parameter,-x, --sparse-exponent- sparse mode exponent.
colord decompress [options] <archive> <output>
Positionals:
input- archive path,output- output file path.
Options:
-h, --help- print help,-G, --reference-genome- optional reference genome path (multi-FASTA gzipped or not), required for reference-based archives with no reference genome embedded (-Gcompression without-sswitch),-v, --verbose- verbose mode.
colord info <archive>