---
name: "splazers"
section: "1"
platform: "linux"
package: "seqan-apps"
version: "2.4.0+dfsg-16"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/splazers"
---

# splazers(1)

Split-map read sequences

## 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*.