---
name: "razers3"
section: "1"
platform: "linux"
package: "seqan-apps"
version: "2.4.0+dfsg-16"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/razers3"
---

# razers3(1)

Faster, fully sensitive read mapping

## 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. Use - to read single-end reads from stdin.

(c) Copyright 2009-2014 by David Weese.

## 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:

- **-i**, **--percent-identity** *DOUBLE*

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

- **-rr**, **--recognition-rate** *DOUBLE*

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

- **-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** *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 \[14..inf\].

- **-o**, **--output** *OUTPUT\_FILE*

  Mapping result filename (use - to dump to stdout in razers format). Default: \<*READS FILE*\>.razers. Valid filetypes are: *.sam*, *.razers*, *.gff*, *.fasta*, *.fa*, *.eland*, *.bam*, and *.afg*.

- **-v**, **--verbose**

  Verbose mode.

- **-vv**, **--vverbose**

  Very verbose mode.

### Paired-end Options:

- **-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*.

### 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** *INTEGER*

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

- **-gn**, **--genome-naming** *INTEGER*

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

- **-rn**, **--read-naming** *INTEGER*

  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** *INTEGER*

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

- **-pf**, **--position-format** *INTEGER*

  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** *STRING*

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

- **-mr**, **--mutation-rate** *DOUBLE*

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

- **-ol**, **--overlap-length** *INTEGER*

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

- **-pd**, **--param-dir** *STRING*

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

- **-t**, **--threshold** *INTEGER*

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

- **-tl**, **--taboo-length** *INTEGER*

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

- **-s**, **--shape** *STRING*

  Manually set k-mer shape.

- **-oc**, **--overabundance-cut** *INTEGER*

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

- **-rl**, **--repeat-length** *INTEGER*

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

- **-lf**, **--load-factor** *DOUBLE*

  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** *STRING*

  Write error distribution to *FILE*.

- **-mf**, **--mismatch-file** *STRING*

  Write mismatch patterns to *FILE*.

### Misc Options:

- **-cm**, **--compact-mult** *DOUBLE*

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

- **-ncf**, **--no-compact-frac** *DOUBLE*

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

### Parallelism Options:

- **-tc**, **--thread-count** *INTEGER*

  Set the number of threads to use (0 to force sequential mode). In range \[0..inf\]. Default: *1*.

- **-pws**, **--parallel-window-size** *INTEGER*

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

- **-pvs**, **--parallel-verification-size** *INTEGER*

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

- **-pvmpc**, **--parallel-verification-max-package-count** *INTEGER*

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

- **-amms**, **--available-matches-memory-size** *INTEGER*

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

- **-mhst**, **--match-histo-start-threshold** *INTEGER*

  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

- .bam

  BAM 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.