Fast read mapping with sensitivity control synopsis razers [options] genome file reads file razers [options] genome file mp-reads file1 mp-reads file2 description razers is a versatile full-sensitive read mapper based on a k-mer counting filter. it supports single and paired-end mapping, and optimally parametrizes the filter based on a user-defined minimal sensitivity. see http://www.seqan.de/projects/razers for more information. input to razers is a reference genome file and either one file with single-end reads or two files containing left or right mates of paired-end reads. (c) copyright 2009 by david weese. -h, --help displays this help message. --version display version information main options: -f, --forward map reads only to forward strands. -r, --reverse map reads only to reverse strands. -i, --percent-identity num percent identity threshold. in range [50..100]. default: 92. -rr, --recognition-rate num percent recognition rate. in range [80..100]. default: 99. -pd, --param-dir dir read user-computed parameter files in the directory dir. -id, --indels allow indels. default: mismatches only. -ll, --library-length num paired-end library length. in range [1..inf]. default: 220. -le, --library-error num paired-end library length tolerance. in range [0..inf]. default: 50. -m, --max-hits num output only num of the best hits. in range [1..inf]. default: 100. --unique output only unique best matches (-m 1 -dr 0 -pa). -tr, --trim-reads num trim reads to given length. default: off. in range [14..inf]. -o, --output file change output filename. default: reads file.razers. valid filetypes are: razers, eland, fa, fasta, and gff. -v, --verbose verbose mode. -vv, --vverbose very verbose mode. output format options: -a, --alignment dump the alignment for each match (only razer or fasta format). -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. -gn, --genome-naming num select how genomes are named (see naming section below). in range [0..1]. default: 0. -rn, --read-naming num select how reads are named (see naming section below). in range [0..2]. default: 0. -so, --sort-order num select how matches are sorted (see sorting section below). in range [0..1]. default: 0. -pf, --position-format num select begin/end position numbering (see coordinate section below). in range [0..1]. default: 0. filtration options: -s, --shape bitstring manually set k-mer shape. default: 11111111111. -t, --threshold num manually set minimum k-mer count threshold. in range [1..inf]. -oc, --overabundance-cut num set k-mer overabundance cut ratio. in range [0..1]. -rl, --repeat-length num skip simple-repeats of length num. in range [1..inf]. default: 1000. -tl, --taboo-length num set taboo length. in range [1..inf]. default: 1. -lm, --low-memory decrease memory usage at the expense of runtime. verification options: -mn, --match-n n matches all other characters. default: n matches nothing. -ed, --error-distr file write error distribution to file. -mcl, --min-clipped-len num set minimal read length for read clipping. in range [0..inf]. default: 0. -qih, --quality-in-header quality string in fasta header. formats, naming, sorting, and coordinate schemes razers supports various output formats. the output format is detected automatically from the file name suffix. .razers razer format .fa, .fasta enhanced fasta format .eland eland format