Author: tille Date: 2013-02-23 11:34:50 +0000 (Sat, 23 Feb 2013) New Revision: 13068
Added: trunk/packages/flexbar/trunk/debian/flexbar.1 trunk/packages/flexbar/trunk/debian/manpages Log: Manpage for flexbar Added: trunk/packages/flexbar/trunk/debian/flexbar.1 =================================================================== --- trunk/packages/flexbar/trunk/debian/flexbar.1 (rev 0) +++ trunk/packages/flexbar/trunk/debian/flexbar.1 2013-02-23 11:34:50 UTC (rev 13068) @@ -0,0 +1,261 @@ +.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.40.10. +.TH FLEXBAR "1" "February 2013" "flexbar version 2.32" "User Commands" +.SH NAME +flexbar \- flexible barcode and adapter removal for sequencing platforms +.SH SYNOPSIS +.IP +flexbar \fB\-t\fR target \fB\-f\fR format \fB\-r\fR +reads [\-b barcodes] [\-a adapters] +[options] +.PP +.SH OPTIONS +.HP +\fB\-h\fR, \fB\-\-help\fR +.IP +Display this help message +.HP +\fB\-v\fR, \fB\-\-version\fR +.IP +Display program version +.HP +\fB\-c\fR, \fB\-\-cite\fR +.IP +View citation information +.IP +Basic options: +.HP +\fB\-n\fR, \fB\-\-threads\fR NUM +.IP +Number of threads, default: +1 +.HP +\fB\-t\fR, \fB\-\-target\fR STR +.IP +Prefix for output file names +.HP +\fB\-r\fR, \fB\-\-reads\fR FILE +.IP +Input file with reads, that +may contain barcodes +.HP +\fB\-p\fR, \fB\-\-reads2\fR FILE +.IP +Second input file for paired +read scenario +.HP +\fB\-f\fR, \fB\-\-format\fR STR +.IP +Input format of reads: +csfasta, csfastq, fasta, +fastq, fastq\-sanger, +fastq\-solexa, fastq\-i1.3, +fastq\-i1.5, fastq\-i1.8 +(illumina 1.8+) +.IP +Barcode detection: +.HP +\fB\-b\fR, \fB\-\-barcodes\fR FILE +.IP +Fasta file with barcodes, +specify (br) to use separate +barcode reads +.HP +\fB\-br\fR, \fB\-\-barcode\-reads\fR FILE +.IP +Fasta or fastq file with +separate barcode reads, if +not within reads +.HP +\fB\-be\fR, \fB\-\-barcode\-trim\-end\fR STR +.IP +Type of barcoding within +reads, see section trim\-end +modes, default: ANY +.HP +\fB\-bn\fR, \fB\-\-barcode\-tail\-length\fR NUM +.IP +Number of bases for tail +trim\-end types, default: +barcode length +.HP +\fB\-bo\fR, \fB\-\-barcode\-min\-overlap\fR NUM +.IP +Minimum overlap of barcode +and read, default: barcode +length +.HP +\fB\-bt\fR, \fB\-\-barcode\-threshold\fR NUM +.IP +Allowed mismatches and +indels per 10 bases for +barcode, default: 1.0 +.HP +\fB\-bk\fR, \fB\-\-barcode\-keep\fR +.IP +Keep barcodes within reads +instead of removal +.HP +\fB\-ba\fR, \fB\-\-barcode\-tag\-length\fR NUM +.IP +Use random code with given +size upstream barcode for +read tagging +.HP +\fB\-bm\fR, \fB\-\-barcode\-match\fR NUM +.IP +Match score, default: 1 +.HP +\fB\-bi\fR, \fB\-\-barcode\-mismatch\fR NUM +.IP +Mismatch score, default: \fB\-1\fR +.HP +\fB\-bg\fR, \fB\-\-barcode\-gap\fR NUM +.IP +Gap score, default: \fB\-7\fR +.IP +Adapter removal: +.HP +\fB\-a\fR, \fB\-\-adapters\fR FILE +.IP +Fasta file with adapters, or +barcodes to remove within +reads +.HP +\fB\-as\fR, \fB\-\-adapter\-seq\fR STR +.IP +Single adapter sequence as +alternative to adapters +option +.HP +\fB\-ae\fR, \fB\-\-adapter\-trim\-end\fR STR +.IP +Type of alignment for +removal, see section +trim\-end modes, default: +RIGHT +.HP +\fB\-an\fR, \fB\-\-adapter\-tail\-length\fR NUM +.IP +Number of bases for tail +trim\-end types, default: +adapter length +.HP +\fB\-ao\fR, \fB\-\-adapter\-min\-overlap\fR NUM +.IP +Minimum overlap of adapter +and read, default: 1 +.HP +\fB\-at\fR, \fB\-\-adapter\-threshold\fR NUM +.IP +Allowed mismatches and +indels per 10 bases for +adapter, default: 3.0 +.HP +\fB\-am\fR, \fB\-\-adapter\-match\fR NUM +.IP +Match score, default: 1 +.HP +\fB\-ai\fR, \fB\-\-adapter\-mismatch\fR NUM +.IP +Mismatch score, default: \fB\-1\fR +.HP +\fB\-ag\fR, \fB\-\-adapter\-gap\fR NUM +.IP +Gap score, default: \fB\-7\fR +.IP +Filtering and trimming: +.HP +\fB\-u\fR, \fB\-\-max\-uncalled\fR NUM +.IP +Allowed uncalled bases (N or +\&.) in reads, default: 0 +.HP +\fB\-x\fR, \fB\-\-pre\-trim\-left\fR NUM +.IP +Trim specified number of +bases on 5' end of reads +before detection +.HP +\fB\-y\fR, \fB\-\-pre\-trim\-right\fR NUM +.IP +Trim specified number of +bases on 3' end of reads +before detection +.HP +\fB\-q\fR, \fB\-\-pre\-trim\-phred\fR NUM +.IP +Trim 3' end until specified +or higher quality reached, +precise fastq format +.HP +\fB\-z\fR, \fB\-\-post\-trim\-length\fR NUM +.IP +Trim to specified read +length from 3' end after +removal +.HP +\fB\-m\fR, \fB\-\-min\-readlength\fR NUM +.IP +Minimum read length to +remain after removal, +default: 18 +.IP +Logging and tagging: +.HP +\fB\-l\fR, \fB\-\-log\-level\fR STR +.IP +Print alignments for all or +modified reads. One of ALL, +MOD, and TAB +.HP +\fB\-s\fR, \fB\-\-single\-reads\fR +.IP +Output single reads of +patially too short paired +reads +.HP +\fB\-d\fR, \fB\-\-length\-dist\fR +.IP +Write length distribution +for read output files +.HP +\fB\-o\fR, \fB\-\-fasta\-output\fR +.IP +Prefer non\-quality formats +fasta and csfasta for output +.HP +\fB\-e\fR, \fB\-\-number\-tags\fR +.IP +Replace read tags by +ascending number to save +space +.HP +\fB\-g\fR, \fB\-\-removal\-tags\fR +.IP +Tag reads that are subject +to adapter or barcode +removal +.IP +Trim\-end modes: +.IP +ANY: longer part of read remains +LEFT: align <= read end, right +part remains +RIGHT: align >= read start, left +part remains +LEFT_TAIL: consider first n bases +of reads in alignment +RIGHT_TAIL: use only last n bases, +see tail\-length options +.PP +.SH EXAMPLES +.IP +flexbar \fB\-t\fR target \fB\-f\fR fastq\-i1.3 \fB\-r\fR +reads.fastq \fB\-b\fR bar.fasta \fB\-a\fR +adap.fasta +.IP +flexbar \fB\-t\fR target \fB\-f\fR csfastq \fB\-r\fR +reads.csfastq \fB\-a\fR adapters.fasta +\fB\-ae\fR LEFT +.PP +Further documentation on: flexbar.sourceforge.net Added: trunk/packages/flexbar/trunk/debian/manpages =================================================================== --- trunk/packages/flexbar/trunk/debian/manpages (rev 0) +++ trunk/packages/flexbar/trunk/debian/manpages 2013-02-23 11:34:50 UTC (rev 13068) @@ -0,0 +1 @@ +debian/*.1 _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
