NAME¶

splazers ======== 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.

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Main Options::

Change output filename. Default: <READS FILE>.result.

only compute forward matches

only compute reverse complement matches

Percent identity threshold. In range [50..100]. Default: 92.

set the percent recognition rate In range [80..100]. Default: 99.

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

Allow indels. Default: mismatches only.

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

Paired-end library length tolerance. In range [0..inf]. Default: 50.

Output only <NUM> of the best hits. In range [1..inf]. Default: 100.

Output only unique best matches (-m 1 -dr 0 -pa).

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

min. read length for read clipping In range [1..inf]. Default: 0.

quality string in fasta header

output filename for unmapped reads

verbose mode

very verbose mode

Output Format Options::

dump the alignment for each match

purge reads with more than max-hits best matches

only consider matches with at most NUM more errors compared to the best (default output all)

Set output format. 0 = RazerS, 1 = Enhanced Fasta, 2 = Eland, 3 = GFF, 4 = SAM. In range [0..4].

Select how genomes are named. 0 = use Fasta id, 1 = enumerate beginning with 1. In range [0..1]. Default: 0.

Select how reads are named. 0 = use Fasta id, 1 = enumerate beginning with 1. In range [0..1]. Default: 0.

Select how matches are sorted. 0 = read number, 1 = genome position. In range [0..1]. Default: 0.

Select begin/end position numbering (see Coordinate section below). 0 = gap space, 1 = position space. In range [0..1]. Default: 0.

Split Mapping Options::

min. match length for prefix/suffix mapping (to disable split mapping, set to 0) Default: 18.

max. length of middle gap Default: 10000.

min. length of middle gap (for edit distance mapping about 10% of read length is recommended) Default: 0.

max. number of errors in prefix match Default: 1.

max. number of errors in suffix match Default: 1.

genome length in Mb, for computation of expected number of random matches In range [-inf..10000]. Default: 3000.

anchored split mapping, only unmapped reads with mapped mates will be considered, requires the reads to be given in SAM format

percent of read length, used as penalty for split-gap Default: 2.

Filtration Options::

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

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

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

decrease memory usage at the expense of runtime

Verification Options:

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

Write error distribution to FILE.

VERSION

splazers version: 1.1 Last update Apr 2011