razers1
Fast read mapping with sensitivity control
Usage
razers [OPTIONS]
<GENOME
FILE>
<READS
FILE>
razers [OPTIONS]
<GENOME
FILE>
<MP-READS
FILE1>
<MP-READS
FILE2>
Overview
RazerS is a versatile full-sensitive read mapper based on a k-mer counting filter. It supports single and paired-end mapping, and optimally parametrizes the filter based on a user-defined minimal sensitivity. See http://www.seqan.de/projects/razers for more information.
Input to RazerS 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.
(c) Copyright 2009 by David Weese.
Required arguments
- ARGUMENT 0 INPUT_FILE
-
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.
- READS List of INPUT_FILE's
-
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.
Options
-
-h, --help -
Display the help message.
-
--version -
Display version information.
Main Options:
-
-f, --forward -
Map reads only to forward strands.
-
-r, --reverse -
Map reads only to reverse strands.
-
-i, --percent-identity DOUBLE -
Percent identity threshold. In range [50..100]. Default: 92.
-
-rr, --recognition-rate DOUBLE -
Percent recognition rate. In range [80..100]. Default: 99.
-
-pd, --param-dir STRING -
Read user-computed parameter files in the directory <DIR>.
-
-id, --indels -
Allow indels. Default: mismatches only.
-
-ll, --library-length INTEGER -
Paired-end library length. In range [1..inf]. Default: 220.
-
-le, --library-error INTEGER -
Paired-end library length tolerance. In range [0..inf]. Default: 50.
-
-m, --max-hits INTEGER -
Output only <NUM> of the best hits. In range [1..inf]. Default: 100.
-
--unique -
Output only unique best matches (-m 1 -dr 0 -pa).
-
-tr, --trim-reads INTEGER -
Trim reads to given length. Default: off. In range [14..inf].
-
-o, --output OUTPUT_FILE -
Change output filename (use - to dump to stdout in razers format). Default: <READS FILE>.razers. Valid filetypes are: .razers, .gff, .fasta, .fa, and .eland.
-
-v, --verbose -
Verbose mode.
-
-vv, --vverbose -
Very verbose mode.
Output Format Options:
-
-a, --alignment -
Dump the alignment for each match (only razer or fasta format).
-
-pa, --purge-ambiguous -
Purge reads with more than <max-hits> best matches.
-
-dr, --distance-range INTEGER -
Only consider matches with at most NUM more errors compared to the best. Default: output all.
-
-gn, --genome-naming INTEGER -
Select how genomes are named (see Naming section below). In range [0..1]. Default: 0.
-
-rn, --read-naming INTEGER -
Select how reads are named (see Naming section below). In range [0..2]. Default: 0.
-
-so, --sort-order INTEGER -
Select how matches are sorted (see Sorting section below). In range [0..1]. Default: 0.
-
-pf, --position-format INTEGER -
Select begin/end position numbering (see Coordinate section below). In range [0..1]. Default: 0.
Filtration Options:
-
-s, --shape STRING -
Manually set k-mer shape. Default: 11111111111.
-
-t, --threshold INTEGER -
Manually set minimum k-mer count threshold. In range [1..inf].
-
-oc, --overabundance-cut INTEGER -
Set k-mer overabundance cut ratio. In range [0..1].
-
-rl, --repeat-length INTEGER -
Skip simple-repeats of length <NUM>. In range [1..inf]. Default: 1000.
-
-tl, --taboo-length INTEGER -
Set taboo length. In range [1..inf]. Default: 1.
-
-lm, --low-memory -
Decrease memory usage at the expense of runtime.
Verification Options:
-
-mN, --match-N -
N matches all other characters. Default: N matches nothing.
-
-ed, --error-distr STRING -
Write error distribution to FILE.
-
-mcl, --min-clipped-len INTEGER -
Set minimal read length for read clipping. In range [0..inf]. Default: 0.
-
-qih, --quality-in-header -
Quality string in fasta header.
Formats, naming, sorting, and coordinate schemes
RazerS supports various output formats. The output format is detected automatically from the file name suffix.
- .razers
-
Razer format
- .fa, .fasta
-
Enhanced Fasta format
- .eland
-
Eland format
- .gff
-
GFF format
By default, reads and contigs are referred by their Fasta ids given in the input files. With the
-gnand-rnoptions this behaviour can be changed:
- 0
-
Use Fasta id.
- 1
-
Enumerate beginning with 1.
- 2
-
Use the read sequence (only for short reads!).
The way matches are sorted in the output file can be changed with the
-sooption for the following formats:razer,fasta,sam, andamos. Primary and secondary sort keys are:
- 0
-
1. read number, 2. genome position
- 1
-
1. genome position, 2. read number
The coordinate space used for begin and end positions can be changed with the
-pfoption for therazerandfastaformats:
- 0
-
Gap space. Gaps between characters are counted from 0.
- 1
-
Position space. Characters are counted from 1.
Examples
razersexample/genome.faexample/reads.fa-id-a-mN-v-
Map single-end reads with 4% error rate, indels, and output the alignments. Ns are considered to match everything.
razersexample/genome.faexample/reads.faexample/reads2.fa-id-mN-
Map paired-end reads with up to 4% errors, indels, and output concordantly mapped pairs within default library size. Ns are considered to match everything.
Releases
8 releases since Debian 6.0 (Squeeze); the text changed 3 times.
--alignment since Debian 10 (Buster);
--distance-range since Debian 10 (Buster);
--error-distr since Debian 10 (Buster);
--forward since Debian 10 (Buster);
--genome-naming since Debian 10 (Buster);
--help since Debian 10 (Buster);
--indels since Debian 10 (Buster);
--library-error since Debian 10 (Buster);
--library-length since Debian 10 (Buster);
--low-memory since Debian 10 (Buster);
--match-N since Debian 10 (Buster);
--max-hits since Debian 10 (Buster);
--min-clipped-len since Debian 10 (Buster);
--output since Debian 10 (Buster);
--overabundance-cut since Debian 10 (Buster);
--param-dir since Debian 10 (Buster);
--percent-identity since Debian 10 (Buster);
--position-format since Debian 10 (Buster);
--purge-ambiguous since Debian 10 (Buster);
--quality-in-header since Debian 10 (Buster);
--read-naming since Debian 10 (Buster);
--recognition-rate since Debian 10 (Buster);
--repeat-length since Debian 10 (Buster);
--reverse since Debian 10 (Buster);
--shape since Debian 10 (Buster);
--sort-order since Debian 10 (Buster);
--taboo-length since Debian 10 (Buster);
--threshold since Debian 10 (Buster);
--trim-reads since Debian 10 (Buster);
--unique since Debian 10 (Buster);
--verbose since Debian 10 (Buster);
--version since Debian 10 (Buster);
--vverbose since Debian 10 (Buster);
-a since Debian 10 (Buster);
-dr since Debian 10 (Buster);
-ed since Debian 10 (Buster);
-f since Debian 10 (Buster);
-gn since Debian 10 (Buster);
-h since Debian 10 (Buster);
-i since Debian 10 (Buster);
-id since Debian 10 (Buster);
-le since Debian 10 (Buster);
-ll since Debian 10 (Buster);
-lm since Debian 10 (Buster);
-m since Debian 10 (Buster);
-mN since Debian 10 (Buster);
-mcl since Debian 10 (Buster);
-o since Debian 10 (Buster);
-oc since Debian 10 (Buster);
-pa since Debian 10 (Buster);
-pd since Debian 10 (Buster);
-pf since Debian 10 (Buster);
-qih since Debian 10 (Buster);
-r since Debian 10 (Buster);
-rl since Debian 10 (Buster);
-rn since Debian 10 (Buster);
-rr since Debian 10 (Buster);
-s since Debian 10 (Buster);
-so since Debian 10 (Buster);
-t since Debian 10 (Buster);
-tl since Debian 10 (Buster);
-tr since Debian 10 (Buster);
-v since Debian 10 (Buster);
-vv since Debian 10 (Buster).
--output-format until Debian 7 (Wheezy);
-V until Debian 7 (Wheezy);
-of until Debian 7 (Wheezy).