Man page - razers3(1)

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• alf(1)
• mason_materializer(1)
• pair_align(1)
• gustaf(1)
• stellar(1)
• razers3(1)
• sak(1)
• yara_indexer(1)
• mason_frag_sequencing(1)
• micro_razers(1)
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• insegt(1)
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• splazers(1)
• seqan_tcoffee(1)
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• razers(1)
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Manual

RAZERS3

NAME
SYNOPSIS
DESCRIPTION
REQUIRED ARGUMENTS
OPTIONS
Main Options:
Paired-end Options:
Output Format Options:
Filtration Options:
Verification Options:
Misc Options:
Parallelism Options:
FORMATS, NAMING, SORTING, AND COORDINATE SCHEMES
EXAMPLES

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NAME

razers3 - Faster, fully sensitive read mapping

SYNOPSIS

razers3 [ OPTIONS ] < GENOME FILE > < READS FILE >
razers3 [ OPTIONS ] < GENOME FILE > < PE-READS FILE1 > < PE-READS FILE2 >

DESCRIPTION

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.

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.

(c) Copyright 2009-2014 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:

-i , --percent-identity DOUBLE

Percent identity threshold. In range [50..100]. Default: 95 .

-rr , --recognition-rate DOUBLE

Percent recognition rate. In range [80..100]. Default: 100 .

-ng , --no-gaps

Allow only mismatches, no indels. Default: allow both.

-f , --forward

Map reads only to forward strands.

-r , --reverse

Map reads only to reverse strands.

-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

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 .

-v , --verbose

Verbose mode.

-vv , --vverbose

Very verbose mode.

Paired-end Options:

-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 .

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..3]. Default: 0 .

--full-readid

Use the whole read id (don’t clip after whitespace).

-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 .

-ds , --dont-shrink-alignments

Disable alignment shrinking in SAM. This is required for generating a gold mapping for Rabema.

Filtration Options:

-fl , --filter STRING

Select k-mer filter. One of pigeonhole and swift . Default: pigeonhole .

-mr , --mutation-rate DOUBLE

Set the percent mutation rate ( pigeonhole ). In range [0..20]. Default: 5 .

-ol , --overlap-length INTEGER

Manually set the overlap length of adjacent k-mers ( pigeonhole ). In range [0..inf].

-pd , --param-dir STRING

Read user-computed parameter files in the directory < DIR > ( swift ).

-t , --threshold INTEGER

Manually set minimum k-mer count threshold ( swift ). In range [1..inf].

-tl , --taboo-length INTEGER

Set taboo length ( swift ). In range [1..inf]. Default: 1 .

-s , --shape STRING

Manually set k-mer shape.

-oc , --overabundance-cut INTEGER

Set k-mer overabundance cut ratio. In range [0..1]. Default: 1 .

-rl , --repeat-length INTEGER

Skip simple-repeats of length < NUM >. In range [1..inf]. Default: 1000 .

-lf , --load-factor DOUBLE

Set the load factor for the open addressing k-mer index. In range [1..inf]. Default: 1.6 .

Verification Options:

-mN , --match-N

N matches all other characters. Default: N matches nothing.

-ed , --error-distr STRING

Write error distribution to FILE .

-mf , --mismatch-file STRING

Write mismatch patterns to FILE .

Misc Options:

-cm , --compact-mult DOUBLE

Multiply compaction threshold by this value after reaching and compacting. In range [0..inf]. Default: 2.2 .

-ncf , --no-compact-frac DOUBLE

Don’t compact if in this last fraction of genome. In range [0..1]. Default: 0.05 .

Parallelism Options:

-tc , --thread-count INTEGER

Set the number of threads to use (0 to force sequential mode). In range [0..inf]. Default: 1 .

-pws , --parallel-window-size INTEGER

Collect candidates in windows of this length. In range [1..inf]. Default: 500000 .

-pvs , --parallel-verification-size INTEGER

Verify candidates in packages of this size. In range [1..inf]. Default: 100 .

-pvmpc , --parallel-verification-max-package-count INTEGER

Largest number of packages to create for verification per thread-1. In range [1..inf]. Default: 100 .

-amms , --available-matches-memory-size INTEGER

Bytes of main memory available for storing matches. In range [-1..inf]. Default: 0 .

-mhst , --match-histo-start-threshold INTEGER

When to start histogram. In range [1..inf]. Default: 5 .

FORMATS, NAMING, SORTING, AND COORDINATE SCHEMES

RazerS 3 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
	.sam		SAM format
	.bam		BAM format
	.afg		Amos AFG format

By default, reads and contigs are referred by their Fasta ids given in the input files. With the -gn and -rn options this behaviour can be changed:

	0		Use Fasta id.
	1		Enumerate beginning with 1.
	2		Use the read sequence (only for short reads!).
	3		Use the Fasta id, do NOT append /L or /R for mate pairs.

The way matches are sorted in the output file can be changed with the -so option for the following formats: razers , fasta , sam , and afg . 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 -pf option for the razer and fasta formats:

	0		Gap space. Gaps between characters are counted from 0.
	1		Position space. Characters are counted from 1.

EXAMPLES

razers3 -i 96 -tc 12 -o mapped.razers hg18.fa reads.fq

Map single-end reads with 4% error rate using 12 threads.

razers3 -i 95 -no-gaps -o mapped.razers hg18.fa reads.fq.gz

Map single-end gzipped reads with 5% error rate and no indels.

razers3 -i 94 -rr 95 -tc 12 -ll 280 --le 80 -o mapped.razers hg18.fa
reads_1.fq reads_2.fq

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.

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