RAZERS3(1)

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.