---
name: "cassiopee"
section: "1"
platform: "linux"
package: "cassiopee"
version: "1.0.9-4+b1"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/cassiopee"
---

# cassiopee(1)

index and search tool in genomic sequences

## 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