--- name: "razers" section: "1" platform: "linux" package: "seqan-apps" version: "2.4.0+dfsg-16" release: "Debian 13 (Trixie)" platforms: ["linux"] url: "https://new.carta.tech/razers" --- # razers(1) Fast Read Mapping with Sensitivity Control ## NAME razers - Fast Read Mapping with Sensitivity Control ## SYNOPSIS **razers** \[*OPTIONS*\] \<*GENOME FILE*\> \<*READS FILE*\>\ **razers** \[*OPTIONS*\] \<*GENOME FILE*\> \<*MP-READS FILE1*\> \<*MP-READS FILE2*\> ## DESCRIPTION RazerS is a versatile full-sensitive read mapper based on a k-mer counting filter. It supports single and paired-end mapping, 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 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 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: - **-f**, **--forward** Map reads only to forward strands. - **-r**, **--reverse** Map reads only to reverse strands. - **-i**, **--percent-identity** *DOUBLE* Percent identity threshold. In range \[50..100\]. Default: *92*. - **-rr**, **--recognition-rate** *DOUBLE* 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 \[14..inf\]. - **-o**, **--output** *OUTPUT\_FILE* Change output filename (use - to dump to stdout in razers format). Default: \<*READS FILE*\>.razers. Valid filetypes are: *.razers*, *.gff*, *.fasta*, *.fa*, and *.eland*. - **-v**, **--verbose** Verbose mode. - **-vv**, **--vverbose** Very verbose mode. ### 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 \[0..2\]. Default: *0*. - **-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*. ### Filtration Options: - **-s**, **--shape** *STRING* Manually set k-mer shape. Default: *11111111111*. - **-t**, **--threshold** *INTEGER* Manually set minimum k-mer count threshold. In range \[1..inf\]. - **-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*. - **-mcl**, **--min-clipped-len** *INTEGER* Set minimal read length for read clipping. In range \[0..inf\]. Default: *0*. - **-qih**, **--quality-in-header** Quality string in fasta header. ## FORMATS, NAMING, SORTING, AND COORDINATE SCHEMES RazerS 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 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!). The way matches are sorted in the output file can be changed with the **-so** option for the following formats: **razer**, **fasta**, **sam**, and **amos**. 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 - **razers** **example/genome.fa** **example/reads.fa** **-id** **-a** **-mN** **-v** Map single-end reads with 4% error rate, indels, and output the alignments. Ns are considered to match everything. - **razers** **example/genome.fa** **example/reads.fa** **example/reads2.fa** **-id** **-mN** Map paired-end reads with up to 4% errors, indels, and output concordantly mapped pairs within default library size. Ns are considered to match everything.