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razers: Fast Read Mapping with Sensitivity Control


RazerS - Fast Read Mapping with Sensitivity Control




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


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 RAZERS(1)

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