razers3(1)

Usage

razers3 [OPTIONS] <GENOME FILE> <READS FILE>

razers3 [OPTIONS] <GENOME FILE> <PE-READS FILE1> <PE-READS FILE2>

Overview

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.

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.

Releases

6 releases since Debian 8 (Jessie); the text changed 2 times.

--alignment since Debian 10 (Buster); --available-matches-memory-size since Debian 10 (Buster); --compact-mult since Debian 10 (Buster); --distance-range since Debian 10 (Buster); --dont-shrink-alignments since Debian 10 (Buster); --error-distr since Debian 10 (Buster); --filter since Debian 10 (Buster); --forward since Debian 10 (Buster); --full-readid since Debian 10 (Buster); --genome-naming since Debian 10 (Buster); --help since Debian 10 (Buster); --library-error since Debian 10 (Buster); --library-length since Debian 10 (Buster); --load-factor since Debian 10 (Buster); --match-N since Debian 10 (Buster); --match-histo-start-threshold since Debian 10 (Buster); --max-hits since Debian 10 (Buster); --mismatch-file since Debian 10 (Buster); --mutation-rate since Debian 10 (Buster); --no-compact-frac since Debian 10 (Buster); --no-gaps since Debian 10 (Buster); --output since Debian 10 (Buster); --overabundance-cut since Debian 10 (Buster); --overlap-length since Debian 10 (Buster); --parallel-verification-max-package-count since Debian 10 (Buster); --parallel-verification-size since Debian 10 (Buster); --parallel-window-size since Debian 10 (Buster); --param-dir since Debian 10 (Buster); --percent-identity since Debian 10 (Buster); --position-format since Debian 10 (Buster); --purge-ambiguous since Debian 10 (Buster); --read-naming since Debian 10 (Buster); --recognition-rate since Debian 10 (Buster); --repeat-length since Debian 10 (Buster); --reverse since Debian 10 (Buster); --shape since Debian 10 (Buster); --sort-order since Debian 10 (Buster); --taboo-length since Debian 10 (Buster); --thread-count since Debian 10 (Buster); --threshold since Debian 10 (Buster); --trim-reads since Debian 10 (Buster); --unique since Debian 10 (Buster); --verbose since Debian 10 (Buster); --version since Debian 10 (Buster); --vverbose since Debian 10 (Buster); -a since Debian 10 (Buster); -amms since Debian 10 (Buster); -cm since Debian 10 (Buster); -dr since Debian 10 (Buster); -ds since Debian 10 (Buster); -ed since Debian 10 (Buster); -f since Debian 10 (Buster); -fl since Debian 10 (Buster); -gn since Debian 10 (Buster); -h since Debian 10 (Buster); -i since Debian 10 (Buster); -le since Debian 10 (Buster); -lf since Debian 10 (Buster); -ll since Debian 10 (Buster); -m since Debian 10 (Buster); -mN since Debian 10 (Buster); -mf since Debian 10 (Buster); -mhst since Debian 10 (Buster); -mr since Debian 10 (Buster); -ncf since Debian 10 (Buster); -ng since Debian 10 (Buster); -o since Debian 10 (Buster); -oc since Debian 10 (Buster); -ol since Debian 10 (Buster); -pa since Debian 10 (Buster); -pd since Debian 10 (Buster); -pf since Debian 10 (Buster); -pvmpc since Debian 10 (Buster); -pvs since Debian 10 (Buster); -pws since Debian 10 (Buster); -r since Debian 10 (Buster); -rl since Debian 10 (Buster); -rn since Debian 10 (Buster); -rr since Debian 10 (Buster); -s since Debian 10 (Buster); -so since Debian 10 (Buster); -t since Debian 10 (Buster); -tc since Debian 10 (Buster); -tl since Debian 10 (Buster); -tr since Debian 10 (Buster); -v since Debian 10 (Buster); -vv since Debian 10 (Buster).