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SPLAZERS(1) SPLAZERS(1)

NAME

splazers - Split-map read sequences

SYNOPSIS

splazers [OPTIONS] <GENOME FILE> <READS FILE>
splazers [OPTIONS] <GENOME FILE> <READS FILE 1> <READS FILE 2>

DESCRIPTION

SplazerS uses a prefix-suffix mapping strategy to split-map read sequences.If a SAM file of mapped reads is given as input, all unmapped but anchoredreads are split-mapped onto anchoring target regions (specify option -an),if a Fasta/q file of reads is given, reads are split-mapped onto the wholereference sequence.

(c) Copyright 2010 by Anne-Katrin Emde.

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::

-o, --output OUTPUT_FILE
Change output filename. Default: <READS FILE>.result.
-f, --forward
only compute forward matches
-r, --reverse
only compute reverse complement matches
-i, --percent-identity DOUBLE
Percent identity threshold. In range [50..100]. Default: 92.
-rr, --recognition-rate DOUBLE
set the 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].
-mcl, --min-clipped-len INTEGER
min. read length for read clipping In range [1..inf]. Default: 0.
-qih, --quality-in-header
quality string in fasta header
-ou, --outputUnmapped OUTPUT_FILE
output filename for unmapped reads
-v, --verbose
verbose mode
-vv, --vverbose
very verbose mode

Output Format Options::

-a, --alignment
dump the alignment for each match
-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)
-of, --output-format INTEGER
Set output format. 0 = RazerS, 1 = Enhanced Fasta, 2 = Eland, 3 = GFF, 4 = SAM. In range [0..4].
-gn, --genome-naming INTEGER
Select how genomes are named. 0 = use Fasta id, 1 = enumerate beginning with 1. In range [0..1]. Default: 0.
-rn, --read-naming INTEGER
Select how reads are named. 0 = use Fasta id, 1 = enumerate beginning with 1. In range [0..1]. Default: 0.
-so, --sort-order INTEGER
Select how matches are sorted. 0 = read number, 1 = genome position. In range [0..1]. Default: 0.
-pf, --position-format INTEGER
Select begin/end position numbering (see Coordinate section below). 0 = gap space, 1 = position space. In range [0..1]. Default: 0.

Split Mapping Options::

-sm, --split-mapping INTEGER
min. match length for prefix/suffix mapping (to disable split mapping, set to 0) Default: 18.
-maxG, --max-gap INTEGER
max. length of middle gap Default: 10000.
-minG, --min-gap INTEGER
min. length of middle gap (for edit distance mapping about 10% of read length is recommended) Default: 0.
-ep, --errors-prefix INTEGER
max. number of errors in prefix match Default: 1.
-es, --errors-suffix INTEGER
max. number of errors in suffix match Default: 1.
-gl, --genome-len INTEGER
genome length in Mb, for computation of expected number of random matches In range [-inf..10000]. Default: 3000.
-an, --anchored
anchored split mapping, only unmapped reads with mapped mates will be considered, requires the reads to be given in SAM format
-pc, --penalty-c INTEGER
percent of read length, used as penalty for split-gap Default: 2.

Filtration Options::

-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.
splazers 1.3.7 [tarball]