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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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