.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.4.
.TH RAZERS3 "1" "June 2017" "razers3 2.3.1+dfsg-4" "User Commands"
.SH NAME
razers3 \- Faster, fully sensitive read mapping
.PP
SYNOPSIS
.IP
razers3 [OPTIONS] <GENOME FILE> <READS FILE>
razers3 [OPTIONS] <GENOME FILE> <PE\-READS FILE1> <PE\-READS FILE2>
.PP
DESCRIPTION
.IP
RazerS 3 is a versatile full\-sensitive read mapper based on k\-mer counting
and seeding filters. It supports single and paired\-end mapping,
shared\-memory parallelism, and optimally parametrizes the filter based on
a user\-defined minimal sensitivity. See
http://www.seqan.de/projects/razers for more information.
.IP
Input to RazerS 3 is a reference genome file and either one file with
single\-end reads or two files containing left or right mates of paired\-end
reads. Use \- to read single\-end reads from stdin.
.IP
(c) Copyright 2009\-2014 by David Weese.
.PP
REQUIRED ARGUMENTS
.IP
ARGUMENT 0 INPUT_FILE
.IP
A reference genome file. Valid filetypes are: .sam[.*], .raw[.*],
\&.gbk[.*], .frn[.*], .fq[.*], .fna[.*], .ffn[.*], .fastq[.*],
\&.fasta[.*], .faa[.*], .fa[.*], .embl[.*], and .bam, where * is any
of the following extensions: gz, bz2, and bgzf for transparent
(de)compression.
.IP
READS List of INPUT_FILE's
.IP
Either one (single\-end) or two (paired\-end) read files. Valid
filetypes are: .sam[.*], .raw[.*], .gbk[.*], .frn[.*], .fq[.*],
\&.fna[.*], .ffn[.*], .fastq[.*], .fasta[.*], .faa[.*], .fa[.*],
\&.embl[.*], and .bam, where * is any of the following extensions: gz,
bz2, and bgzf for transparent (de)compression.
.PP
OPTIONS
.HP
\fB\-h\fR, \fB\-\-help\fR
.IP
Display the help message.
.HP
\fB\-\-version\-check\fR BOOL
.IP
Turn this option off to disable version update notifications of the
application. One of 1, ON, TRUE, T, YES, 0, OFF, FALSE, F, and NO.
Default: 1.
.HP
\fB\-\-version\fR
.IP
Display version information.
.IP
Main Options:
.HP
\fB\-i\fR, \fB\-\-percent\-identity\fR DOUBLE
.IP
Percent identity threshold. In range [50..100]. Default: 95.
.HP
\fB\-rr\fR, \fB\-\-recognition\-rate\fR DOUBLE
.IP
Percent recognition rate. In range [80..100]. Default: 100.
.HP
\fB\-ng\fR, \fB\-\-no\-gaps\fR
.IP
Allow only mismatches, no indels. Default: allow both.
.HP
\fB\-f\fR, \fB\-\-forward\fR
.IP
Map reads only to forward strands.
.HP
\fB\-r\fR, \fB\-\-reverse\fR
.IP
Map reads only to reverse strands.
.HP
\fB\-m\fR, \fB\-\-max\-hits\fR INTEGER
.IP
Output only <NUM> of the best hits. In range [1..inf]. Default: 100.
.HP
\fB\-\-unique\fR
.IP
Output only unique best matches (\fB\-m\fR 1 \fB\-dr\fR 0 \fB\-pa\fR).
.HP
\fB\-tr\fR, \fB\-\-trim\-reads\fR INTEGER
.IP
Trim reads to given length. Default: off. In range [14..inf].
.HP
\fB\-o\fR, \fB\-\-output\fR OUTPUT_FILE
.IP
Mapping result filename (use \- to dump to stdout in razers format).
Default: <READS FILE>.razers. Valid filetypes are: .sam, .razers,
\&.gff, .fasta, .fa, .eland, .bam, and .afg.
.HP
\fB\-v\fR, \fB\-\-verbose\fR
.IP
Verbose mode.
.HP
\fB\-vv\fR, \fB\-\-vverbose\fR
.IP
Very verbose mode.
.IP
Paired\-end Options:
.HP
\fB\-ll\fR, \fB\-\-library\-length\fR INTEGER
.IP
Paired\-end library length. In range [1..inf]. Default: 220.
.HP
\fB\-le\fR, \fB\-\-library\-error\fR INTEGER
.IP
Paired\-end library length tolerance. In range [0..inf]. Default: 50.
.IP
Output Format Options:
.HP
\fB\-a\fR, \fB\-\-alignment\fR
.IP
Dump the alignment for each match (only razer or fasta format).
.HP
\fB\-pa\fR, \fB\-\-purge\-ambiguous\fR
.IP
Purge reads with more than <max\-hits> best matches.
.HP
\fB\-dr\fR, \fB\-\-distance\-range\fR INTEGER
.IP
Only consider matches with at most NUM more errors compared to the
best. Default: output all.
.HP
\fB\-gn\fR, \fB\-\-genome\-naming\fR INTEGER
.IP
Select how genomes are named (see Naming section below). In range
[0..1]. Default: 0.
.HP
\fB\-rn\fR, \fB\-\-read\-naming\fR INTEGER
.IP
Select how reads are named (see Naming section below). In range
[0..3]. Default: 0.
.HP
\fB\-\-full\-readid\fR
.IP
Use the whole read id (don't clip after whitespace).
.HP
\fB\-so\fR, \fB\-\-sort\-order\fR INTEGER
.IP
Select how matches are sorted (see Sorting section below). In range
[0..1]. Default: 0.
.HP
\fB\-pf\fR, \fB\-\-position\-format\fR INTEGER
.IP
Select begin/end position numbering (see Coordinate section below).
In range [0..1]. Default: 0.
.HP
\fB\-ds\fR, \fB\-\-dont\-shrink\-alignments\fR
.IP
Disable alignment shrinking in SAM. This is required for generating
a gold mapping for Rabema.
.IP
Filtration Options:
.HP
\fB\-fl\fR, \fB\-\-filter\fR STRING
.IP
Select k\-mer filter. One of pigeonhole and swift. Default:
pigeonhole.
.HP
\fB\-mr\fR, \fB\-\-mutation\-rate\fR DOUBLE
.IP
Set the percent mutation rate (pigeonhole). In range [0..20].
Default: 5.
.HP
\fB\-ol\fR, \fB\-\-overlap\-length\fR INTEGER
.IP
Manually set the overlap length of adjacent k\-mers (pigeonhole). In
range [0..inf].
.HP
\fB\-pd\fR, \fB\-\-param\-dir\fR STRING
.IP
Read user\-computed parameter files in the directory <DIR> (swift).
.HP
\fB\-t\fR, \fB\-\-threshold\fR INTEGER
.IP
Manually set minimum k\-mer count threshold (swift). In range
[1..inf].
.HP
\fB\-tl\fR, \fB\-\-taboo\-length\fR INTEGER
.IP
Set taboo length (swift). In range [1..inf]. Default: 1.
.HP
\fB\-s\fR, \fB\-\-shape\fR STRING
.IP
Manually set k\-mer shape.
.HP
\fB\-oc\fR, \fB\-\-overabundance\-cut\fR INTEGER
.IP
Set k\-mer overabundance cut ratio. In range [0..1]. Default: 1.
.HP
\fB\-rl\fR, \fB\-\-repeat\-length\fR INTEGER
.IP
Skip simple\-repeats of length <NUM>. In range [1..inf]. Default:
1000.
.HP
\fB\-lf\fR, \fB\-\-load\-factor\fR DOUBLE
.IP
Set the load factor for the open addressing k\-mer index. In range
[1..inf]. Default: 1.6.
.IP
Verification Options:
.HP
\fB\-mN\fR, \fB\-\-match\-N\fR
.IP
N matches all other characters. Default: N matches nothing.
.HP
\fB\-ed\fR, \fB\-\-error\-distr\fR STRING
.IP
Write error distribution to FILE.
.HP
\fB\-mf\fR, \fB\-\-mismatch\-file\fR STRING
.IP
Write mismatch patterns to FILE.
.IP
Misc Options:
.HP
\fB\-cm\fR, \fB\-\-compact\-mult\fR DOUBLE
.IP
Multiply compaction threshold by this value after reaching and
compacting. In range [0..inf]. Default: 2.2.
.HP
\fB\-ncf\fR, \fB\-\-no\-compact\-frac\fR DOUBLE
.IP
Don't compact if in this last fraction of genome. In range [0..1].
Default: 0.05.
.IP
Parallelism Options:
.HP
\fB\-tc\fR, \fB\-\-thread\-count\fR INTEGER
.IP
Set the number of threads to use (0 to force sequential mode). In
range [0..inf]. Default: 1.
.HP
\fB\-pws\fR, \fB\-\-parallel\-window\-size\fR INTEGER
.IP
Collect candidates in windows of this length. In range [1..inf].
Default: 500000.
.HP
\fB\-pvs\fR, \fB\-\-parallel\-verification\-size\fR INTEGER
.IP
Verify candidates in packages of this size. In range [1..inf].
Default: 100.
.HP
\fB\-pvmpc\fR, \fB\-\-parallel\-verification\-max\-package\-count\fR INTEGER
.IP
Largest number of packages to create for verification per thread\-1.
In range [1..inf]. Default: 100.
.HP
\fB\-amms\fR, \fB\-\-available\-matches\-memory\-size\fR INTEGER
.IP
Bytes of main memory available for storing matches. In range
[\-1..inf]. Default: 0.
.HP
\fB\-mhst\fR, \fB\-\-match\-histo\-start\-threshold\fR INTEGER
.IP
When to start histogram. In range [1..inf]. Default: 5.
.PP
FORMATS, NAMING, SORTING, AND COORDINATE SCHEMES
.IP
RazerS 3 supports various output formats. The output format is detected
automatically from the file name suffix.
.IP
\&.razers
.IP
Razer format
.IP
\&.fa, .fasta
.IP
Enhanced Fasta format
.IP
\&.eland
.IP
Eland format
.TP
\&.gff
GFF format
.TP
\&.sam
SAM format
.TP
\&.bam
BAM format
.TP
\&.afg
Amos AFG format
.IP
By default, reads and contigs are referred by their Fasta ids given in the
input files. With the \fB\-gn\fR and \fB\-rn\fR options this behaviour can be changed:
.TP
0
Use Fasta id.
.TP
1
Enumerate beginning with 1.
.TP
2
Use the read sequence (only for short reads!).
.TP
3
Use the Fasta id, do NOT append \fI\,/L\/\fP or \fI\,/R\/\fP for mate pairs.
.IP
The way matches are sorted in the output file can be changed with the \fB\-so\fR
option for the following formats: razers, fasta, sam, and afg. Primary and
secondary sort keys are:
.TP
0
1. read number, 2. genome position
.TP
1
1. genome position, 2. read number
.IP
The coordinate space used for begin and end positions can be changed with
the \fB\-pf\fR option for the razer and fasta formats:
.TP
0
Gap space. Gaps between characters are counted from 0.
.TP
1
Position space. Characters are counted from 1.
.PP
EXAMPLES
.IP
razers3 \fB\-i\fR 96 \fB\-tc\fR 12 \fB\-o\fR mapped.razers hg18.fa reads.fq
.IP
Map single\-end reads with 4% error rate using 12 threads.
.IP
razers3 \fB\-i\fR 95 \fB\-no\-gaps\fR \fB\-o\fR mapped.razers hg18.fa reads.fq.gz
.IP
Map single\-end gzipped reads with 5% error rate and no indels.
.IP
razers3 \fB\-i\fR 94 \fB\-rr\fR 95 \fB\-tc\fR 12 \fB\-ll\fR 280 \fB\-\-le\fR 80 \fB\-o\fR mapped.razers hg18.fa reads_1.fq reads_2.fq
.IP
Map paired\-end reads with up to 6% errors, 95% sensitivity, 12
threads, and only output aligned pairs with an outer distance of
200\-360bp.
.PP
VERSION
.IP
Last update:
razers3 version: 3.5.6 [tarball]
SeqAn version: 2.3.1