Man page - cassiopee(1)
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Manual
CASSIOPEE
NAMESYNOPSIS
DESCRIPTION
OPTIONS
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 |