RAZERS(1)

NAME
RazerS - Fast Read Mapping with Sensitivity Control

SYNOPSIS
razers [OPTION]... <GENOME FILE> <READS FILE>

DESCRIPTION
RazerS - Fast Read Mapping with Sensitivity Control

    razers [OPTION]... <GENOME FILE> <MP-READS FILE1> <MP-READS FILE2>

-h,  --help
    displays this help message

-V,  --version
    print version information

  Main Options:

-f,  --forward
    only compute forward matches

-r,  --reverse
    only compute reverse complement matches

-i,  --percent-identity NUM
    set the percent identity threshold (default 92)

-rr, --recognition-rate NUM
    set the percent recognition rate (default 99)

-pd, --param-dir DIR
    folder containing user-computed parameter files (optional)

-id, --indels
    allow indels (default: mismatches only)

-ll, --library-length NUM
    mate-pair library length (default 220)

-le, --library-error NUM
    mate-pair library length tolerance (default 50)

-m,  --max-hits NUM
    output only NUM of the best hits (default 100)

--unique
    output only unique best matches (-m 1 -dr 0 -pa)

-tr, --trim-reads NUM
    trim reads to given length (default off)

-o,  --output FILE
    change output filename (default <READS FILE>.result)

-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 NUM
    only consider matches with at most NUM more errors compared to the best (default output all)

-of, --output-format NUM
    set output format (default 0) 0 = Razer format 1 = enhanced Fasta format 2 = Eland format 3 = GFF format

-gn, --genome-naming NUM
    select how genomes are named (default 0) 0 = use Fasta id 1 = enumerate beginning with 1

-rn, --read-naming NUM
    select how reads are named (default 0) 0 = use Fasta id 1 = enumerate beginning with 1 2 = use the read sequence (only for short reads!)

-so, --sort-order NUM
    select how matches are sorted (default 0) 0 = 1. read number, 2. genome position 1 = 1. genome position, 2. read number

-pf, --position-format NUM
    select begin/end position numbering (default 0) 0 = gap space 1 = position space

  Filtration Options:

-s,  --shape BITSTRING
    set k-mer shape (default 11111111111)

-t,  --threshold NUM
    set minimum k-mer threshold (default 1)

-oc, --overabundance-cut NUM
    set k-mer overabundance cut ratio (default 1)

-rl, --repeat-length NUM
    set simple-repeat length threshold (default 1000)

-tl, --taboo-length NUM
    set taboo length (default 1)

  Verification Options:

-mN, --match-N
    'N' matches with all other characters

-ed, --error-distr FILE
    write error distribution to FILE

AUTHOR
razers was written by David Weese.

This manual page was generated using html2man and polished by Soeren Sonnenburg <sonne@debian.org>, for the Debian project (but may be used by others).