Splazers ======== synopsis splazers [options] genome file reads file splazers [options] genome file reads file 1 reads file 2 description splazers uses a prefix-suffix mapping strategy to split-map read sequences.if a sam file of mapped reads is given as input, all unmapped but anchoredreads are split-mapped onto anchoring target regions (specify option -an),if a fasta/q file of reads is given, reads are split-mapped onto the wholereference sequence. (c) copyright 2010 by anne-katrin emde. -h, --help displays this help message. --version display version information main options:: -o, --output file change output filename. default: reads file.result. -f, --forward only compute forward matches -r, --reverse only compute reverse complement matches -i, --percent-identity num percent identity threshold. in range [50..100]. default: 92. -rr, --recognition-rate num set the 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]. -mcl, --min-clipped-len num min. read length for read clipping in range [1..inf]. default: 0. -qih, --quality-in-header quality string in fasta header -ou, --outputunmapped file output filename for unmapped reads -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. 0 = razers, 1 = enhanced fasta, 2 = eland, 3 = gff, 4 = sam. in range [0..4]. -gn, --genome-naming num select how genomes are named. 0 = use fasta id, 1 = enumerate beginning with 1. in range [0..1]. default: 0. -rn, --read-naming num select how reads are named. 0 = use fasta id, 1 = enumerate beginning with 1. in range [0..1]. default: 0. -so, --sort-order num select how matches are sorted. 0 = read number, 1 = genome position. in range [0..1]. default: 0. -pf, --position-format num select begin/end position numbering (see coordinate section below). 0 = gap space, 1 = position space. in range [0..1]. default: 0. split mapping options:: -sm, --split-mapping num min. match length for prefix/suffix mapping (to disable split mapping, set to 0) default: 18. -maxg, --max-gap num max. length of middle gap default: 10000. -ming, --min-gap num min. length of middle gap (for edit distance mapping about 10% of read length is recommended) default: 0. -ep, --errors-prefix num max. number of errors in prefix match default: 1. -es, --errors-suffix num max. number of errors in suffix match default: 1. -gl, --genome-len num genome length in mb, for computation of expected number of random matches in range [-inf..10000]. default: 3000. -an, --anchored anchored split mapping, only unmapped reads with mapped mates will be considered, requires the reads to be given in sam format -pc, --penalty-c num percent of read length, used as penalty for split-gap default: 2. filtration options:: -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. version splazers version: 1.1 last update apr 2011