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razers

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).