1package "nucmer" 2description "nucmer generates nucleotide alignments between two mutli-FASTA input 3files. The out.delta output file lists the distance between insertions 4and deletions that produce maximal scoring alignments between each 5sequence. The show-* utilities know how to read this format. 6 7By default, nucmer uses anchor matches that are unique in in the 8reference but not necessarily unique in the query. See --mum and 9--maxmatch for different bevahiors." 10 11option("mum") { 12 description "Use anchor matches that are unique in both the reference and query" 13 off } 14option("maxmatch") { 15 description "Use all anchor matches regardless of their uniqueness" 16 off; conflict "mum" } 17option("b", "breaklen") { 18 description "Set the distance an alignment extension will attempt to extend poor scoring regions before giving up" 19 uint32; default 200 } 20option("c", "mincluster") { 21 description "Sets the minimum length of a cluster of matches" 22 uint32; default 65 } 23option("D", "diagdiff") { 24 description "Set the maximum diagonal difference between two adjacent anchors in a cluster" 25 uint32; default 5 } 26option("d", "diagfactor") { 27 description "Set the maximum diagonal difference between two adjacent anchors in a cluster as a differential fraction of the gap length" 28 double; default 0.12 } 29option("noextend") { 30 description "Do not perform cluster extension step" 31 off } 32option("f", "forward") { 33 description "Use only the forward strand of the Query sequences" 34 off } 35option("g", "maxgap") { 36 description "Set the maximum gap between two adjacent matches in a cluster" 37 uint32; default 90 } 38option("l", "minmatch") { 39 description "Set the minimum length of a single exact match" 40 uint32; default 20 } 41option("L", "minalign") { 42 description "Minimum length of an alignment, after clustering and extension" 43 uint32; default 0 } 44option("nooptimize") { 45 description "No alignment score optimization, i.e. if an alignment extension reaches the end of a sequence, it will not backtrack to optimize the alignment score and instead terminate the alignment at the end of the sequence" 46 off } 47option("r", "reverse") { 48 description "Use only the reverse complement of the Query sequences" 49 off; conflict "forward" } 50option("nosimplify") { 51 description "Don't simplify alignments by removing shadowed clusters. Use this option when aligning a sequence to itself to look for repeats" 52 off } 53option("p", "prefix") { 54 description "Write output to PREFIX.delta" 55 string; typestr "PREFIX"; default "out" } 56option("delta") { 57 description "Output delta file to PATH (instead of PREFIX.delta)" 58 c_string; typestr "PATH"; conflict "prefix" } 59option("sam-short") { 60 description "Output SAM file to PATH, short format" 61 c_string; typestr "PATH"; conflict "prefix", "delta" } 62option("sam-long") { 63 description "Output SAM file to PATH, long format" 64 c_string; typestr "PATH"; conflict "prefix", "delta", "sam-short" } 65option("save") { 66 description "Save suffix array to files starting with PREFIX" 67 string; typestr "PREFIX" } 68option("load") { 69 description "Load suffix array from file starting with PREFIX" 70 string; typestr "PREFIX" } 71option("batch") { 72 description "Proceed by batch of chunks of BASES from the reference" 73 uint64; typestr "BASES" 74 conflict "save", "load" } 75option("t", "threads") { 76 description "Use NUM threads (# of cores)" 77 uint32; typestr "NUM" } 78 79# Hidden / experimental options 80option("banded") { 81 description "Enforce absolute banding of dynamic programming matrix based on diagdiff parameter" 82 off; hidden } 83option("large") { 84 description "Force the use of large offsets" 85 off; hidden } 86option("G", "genome") { 87 description "Map genome to genome (long query sequences)" 88 off; hidden } 89option("M", "max-chunk") { 90 description "Max chunk. Stop adding sequence for a thread if more than MAX already." 91 uint64; typestr "MAX"; default 50000; hidden } 92 93arg("ref") { 94 description "Reference sequence file" 95 c_string; typestr "path" } 96arg("qry") { 97 description "Query sequence file" 98 c_string; typestr "path" 99 multiple; } 100