.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.45.1.
.TH VELVETH "1" "July 2014" "velveth 1.2.10+dfsg1" "User Commands"
.SH NAME
velveth \- simple hashing program
.SH DESCRIPTION
velveth \- simple hashing program
Version 1.2.09
.SH OPTIONS
.TP
\fB\-strand_specific\fR
: for strand specific transcriptome sequencing data (default: off)
.TP
\fB\-reuse_Sequences\fR
: reuse Sequences file (or link) already in directory (no need to provide original filenames in this case (default: off)
.TP
\fB\-reuse_binary\fR
: reuse binary sequences file (or link) already in directory (no need to provide original filenames in this case (default: off)
.TP
\fB\-noHash\fR
: simply prepare Sequences file, do not hash reads or prepare Roadmaps file (default: off)
.TP
\fB\-create_binary\fR
: create binary CnyUnifiedSeq file (default: off)
.PP
Synopsis:
.SS "- Short single end reads:"
.IP
velveth Assem 29 \fB\-short\fR \fB\-fastq\fR s_1_sequence.txt
.SS "- Paired-end short reads (remember to interleave paired reads):"
.IP
velveth Assem 31 \fB\-shortPaired\fR \fB\-fasta\fR interleaved.fna
.PP
\- Paired\-end short reads (using separate files for the paired reads)
.IP
velveth Assem 31 \fB\-shortPaired\fR \fB\-fasta\fR \fB\-separate\fR left.fa right.fa
.SS "- Two channels and some long reads:"
.IP
velveth Assem 43 \fB\-short\fR \fB\-fastq\fR unmapped.fna \fB\-longPaired\fR \fB\-fasta\fR SangerReads.fasta
.SS "- Three channels:"
.IP
velveth Assem 35 \fB\-shortPaired\fR \fB\-fasta\fR pe_lib1.fasta \fB\-shortPaired2\fR pe_lib2.fasta \fB\-short3\fR se_lib1.fa
.SS "Output:"
.IP
directory/Roadmaps
directory/Sequences
.IP
[Both files are picked up by graph, so please leave them there]
.SH COPYRIGHT
Copyright 2007, 2008 Daniel Zerbino (zerbino@ebi.ac.uk)
.br
This is free software; see the source for copying conditions.  There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
.PP
Compilation settings:
CATEGORIES = 2
MAXKMERLENGTH = 31
.PP
Usage:
\&./velveth directory hash_length {[\-file_format][\-read_type][\-separate|\-interleaved] filename1 [filename2 ...]} {...} [options]
.TP
directory
: directory name for output files
.TP
hash_length
: EITHER an odd integer (if even, it will be decremented) <= 31 (if above, will be reduced)
: OR: m,M,s where m and M are odd integers (if not, they will be decremented) with m < M <= 31 (if above, will be reduced)
.IP
and s is a step (even number). Velvet will then hash from k=m to k=M with a step of s
.TP
filename
: path to sequence file or \- for standard input
.SS "File format options:"
.HP
\fB\-fasta\fR  \fB\-fastq\fR  \fB\-raw\fR    \fB\-fasta\fR.gz       \fB\-fastq\fR.gz       \fB\-raw\fR.gz \fB\-sam\fR    \fB\-bam\fR    \fB\-fmtAuto\fR
.IP
(Note: \fB\-fmtAuto\fR will detect fasta or fastq, and will try the following programs for decompression : gunzip, pbunzip2, bunzip2
.SS "File layout options for paired reads (only for fasta and fastq formats):"
.TP
\fB\-interleaved\fR
: File contains paired reads interleaved in the one file (default)
.TP
\fB\-separate\fR
: Read 2 separate files for paired reads
.SS "Read type options:"
.HP
\fB\-short\fR  \fB\-shortPaired\fR
.HP
\fB\-short2\fR \fB\-shortPaired2\fR
.HP
\fB\-long\fR   \fB\-longPaired\fR
.HP
\fB\-reference\fR