Man page - gt-compreads-refcompress(1)
Packages contains this manual
- gt-readjoiner(1)
- gt-cds(1)
- gt-extractfeat(1)
- gt-dupfeat(1)
- gt-select(1)
- gt-encseq(1)
- gt-matstat(1)
- gt-md5_to_id(1)
- gt-seqmutate(1)
- gt-seqtranslate(1)
- gt-mkfeatureindex(1)
- gt-dot(1)
- gt-compreads-decompress(1)
- gt-compreads-refcompress(1)
- gt-condenseq(1)
- gt-readjoiner-prefilter(1)
- gt-seqstat(1)
- gt-readjoiner-overlap(1)
- gt-splicesiteinfo(1)
- gt-prebwt(1)
- gt-extractseq(1)
- gt-encseq2spm(1)
- gt-convertseq(1)
- gt-clean(1)
- gt-encseq-encode(1)
- gt-ltrclustering(1)
- gt-seq(1)
- gt-ltrharvest(1)
- gt-sequniq(1)
- gt-inlineseq_split(1)
- gt-mergefeat(1)
- gt-splitfasta(1)
- gt-gtf_to_gff3(1)
- gt-ltrdigest(1)
- gt-seqfilter(1)
- gt-featureindex(1)
- gt-inlineseq_add(1)
- gt-speck(1)
- gt-mmapandread(1)
- gt-tallymer-mkindex(1)
- gt-seed_extend(1)
- gt-hop(1)
- gt-sketch(1)
- gt-repfind(1)
- gt-shulengthdist(1)
- gt-sketch_page(1)
- gt-gff3(1)
- gt-stat(1)
- gt-gff3validator(1)
- gt-packedindex(1)
- gt-merge(1)
- gt-wtree(1)
- gt-encseq-bitextract(1)
- gt-seqids(1)
- gt-readjoiner-assembly(1)
- gt-tirvish(1)
- gt-uniquesub(1)
- gt-encseq-sample(1)
- gt-chseqids(1)
- gt-compreads-compress(1)
- gt-scriptfilter(1)
- gt-seqtransform(1)
- gt-eval(1)
- gt-genomediff(1)
- gt-congruence(1)
- gt-chain2dim(1)
- gt-tallymer(1)
- gt-tagerator(1)
- gt-loccheck(1)
- gt-encseq-info(1)
- gt-snpper(1)
- gt-bed_to_gff3(1)
- gt(1)
- gt-matchtool(1)
- gt-simreads(1)
- gt-csa(1)
- gt-tallymer-occratio(1)
- gt-encseq-check(1)
- gt-tallymer-search(1)
- gt-encseq-bench(1)
- gt-shredder(1)
- gt-gff3_to_gtf(1)
- gt-orffinder(1)
- gt-encseq-decode(1)
- gt-compreads(1)
- gt-encseq-md5(1)
- gt-uniq(1)
- gt-congruence-spacedseed(1)
- gt-id_to_md5(1)
- gt-seqorder(1)
- gt-compreads-refdecompress(1)
- gt-fingerprint(1)
- gt-fastq_sample(1)
- gt-interfeat(1)
apt-get install genometools
Manual
GT-COMPREADS-REFCO
NAMESYNOPSIS
DESCRIPTION
REPORTING BUGS
NAME
gt-compreads-refcompress - Generates compact encoding for fastq data using Reference Compressed Reads (RCR).
SYNOPSIS
gt compreads refcompress [option ...] (-bam file -ref file)
DESCRIPTION
-v [ yes|no ]
be verbose (default: no)
-mquals [ yes|no ]
store mapping quality for each read (default: no)
-quals [ yes|no ]
store all quality values for each read, this implies enabling of option "vquals" (default: no)
-vquals [ yes|no ]
store quality values of read positions having variations compared to reference (default: no)
-descs [ yes|no ]
store read name for each read (default: no)
-ureads [ yes|no ]
store unmapped reads in a separated fastq file (base name will be the value given in name and suffix will be " _unmapped.fastq" (default: no)
-ref [ string ]
Index file (generated by the gt encseq tool) for reference genome. (default: undefined)
-bam [ string ]
File containing alignment of reads to genome (sorted ".bam" file). (default: undefined)
-name [ string ]
specify base name for RCR to be generated. If not set, base name will be set to base name of value given for option "bam" (default: undefined)
-help
display help and exit
-version
display version information and exit
REPORTING BUGS
Report bugs to https://github.com/genometools/genometools/issues.