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razers
Langue: en
Version: September 2009 (ubuntu - 24/10/10)
Section: 1 (Commandes utilisateur)
Sommaire
NAME
RazerS - Fast Read Mapping with Sensitivity ControlSYNOPSIS
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.
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