Masai mapper synopsis masai_mapper [options] genome file reads file description masai is a fast and accurate read mapper based on approximate seeds and multiple backtracking. see http://www.seqan.de/projects/masai for more information. (c) copyright 2011-2012 by enrico siragusa. -h, --help displays this help message. --version display version information mapping options: -mm, --mapping-mode str select mapping mode. one of all, all-best, and any-best. default: any-best. -mb, --mapping-block num maximum number of reads to be mapped at once. in range [10000..inf]. default: 2147483647. -e, --errors num maximum number of errors per read. in range [0..32]. default: 5. -sl, --seed-length num minimum seed length. in range [10..100]. default: 33. -ng, --no-gaps do not align reads with gaps. genome index options: -x, --index str select the genome index type. one of esa, sa, qgram, and fm. default: sa. -xp, --index-prefix str specify an genome index prefix name. default: use the genome filename prefix. output options: -o, --output-file file specify an output file. default: use the reads filename prefix. valid filetypes are: raw and sam. -nc, --no-cigar do not output cigar string. this only affects sam output. debug options: -nv, --no-verify do not verify seed hits. -nd, --no-dump do not dump results. -nm, --no-multiple disable multiple backtracking. version masai_mapper version: 0.7.1 [14053] last update 2013-05-16