razers3 - Online in the Cloud

PROGRAM:

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.

(c) Copyright 2009-2013 by David Weese.

-h, --help

Displays this help message.

--version

Display version information

Main Options:

-i, --percent-identity NUM

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

-rr, --recognition-rate NUM

Percent recognition rate. In range [80..100]. Default: 99.

-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 NUM

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 NUM

Trim reads to given length. Default: off. In range [14..inf].

-o, --output FILE

Mapping result filename. Default: <READS FILE>.razers. Valid filetypes are:
.razers, .eland, .fa, .fasta, .gff, .sam, and .afg.

-v, --verbose

Verbose mode.

-vv, --vverbose

Very verbose mode.

Paired-end Options:

-ll, --library-length NUM

Paired-end library length. In range [1..inf]. Default: 220.

-le, --library-error NUM

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 NUM

Only consider matches with at most NUM more errors compared to the best. Default:
output all.

-gn, --genome-naming NUM

Select how genomes are named (see Naming section below). In range [0..1]. Default:
0.

-rn, --read-naming NUM

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 NUM

Select how matches are sorted (see Sorting section below). In range [0..1].
Default: 0.

-pf, --position-format NUM

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 STR

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

-mr, --mutation-rate NUM

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

-ol, --overlap-length NUM

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

-pd, --param-dir DIR

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

-t, --threshold NUM

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

-tl, --taboo-length NUM

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

-s, --shape BITSTRING

Manually set k-mer shape.

-oc, --overabundance-cut NUM

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

-rl, --repeat-length NUM

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

-lf, --load-factor NUM

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 FILE

Write error distribution to FILE.

-mf, --mismatch-file FILE

Write mismatch patterns to FILE.

Misc Options:

-cm, --compact-mult NUM

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

-ncf, --no-compact-frac NUM

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

Parallelism Options:

-pws, --parallel-window-size NUM

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

-pvs, --parallel-verification-size NUM

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

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

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

-amms, --available-matches-memory-size NUM

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

-mhst, --match-histo-start-threshold NUM

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

.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.

VERSION

razers3 version: 3.2 [14104] Last update 2013-06-12

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