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cassiopee - index and search tool in genomic sequences

CASSIOPEE(1) User Commands CASSIOPEE(1)

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

-l: maximum index depth / maximum pattern size
-u: save index for later use
-s: sequence to index
-p: pattern to search
-f: file containing pattern to search
-o: output file
-r: apply tree reduction
-m: search mode: 0=DNA, 1=RNA, 2=Protein
-a: allow alphabet ambiguity search
-n: max consecutive N allowed matches in search
-e: max substitution allowed matches in search
-i: max indel allowed matches in search
-g: generates a dot file of the graph
-d: max depth of the graph
-t: output format: 0:tsv (default), 1:json
-x: minimum position in sequence
-y: maximum position in sequence
-v: show version
-h: show this message
April 2014 Cassiopee Version 1.0