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).
RazerS version 1.0 20090710 [473September 2009