cassiopee(1)
index and search tool in genomic sequences
Description
CASSIOPEE
NAME
cassiopee - index and search tool in genomic sequences
SYNOPSIS
cassiopee [Options] <sequence>
DESCRIPTION
Cassiopee index and search library C implementation. It is a complete rewrite of the ruby Cassiopee gem. It scans an input genomic sequence (dna/rna/protein) and search for a subsequence with exact match or allowing substitutions (Hamming distance) and/or insertion/deletions.
OPTIONS
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-l: maximum index depth / maximum pattern size |
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-u: save index for later use |
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-s: sequence to index |
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-p: pattern to search |
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-f: file containing pattern to search |
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-o: output file |
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-r: apply tree reduction |
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-m: search mode: 0=DNA, 1=RNA, 2=Protein |
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-a: allow alphabet ambiguity search |
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-n: max consecutive N allowed matches in search |
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-e: max substitution allowed matches in search |
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-i: max indel allowed matches in search |
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-g: generates a dot file of the graph |
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-d: max depth of the graph |
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-t: output format: 0:tsv (default), 1:json |
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-x: minimum position in sequence |
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-y: maximum position in sequence |
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-v: show version |
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-h: show this message |