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

Cassiopee Version 1.0                              April 2014                                       CASSIOPEE(1)