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Covest estimates the coverage and genom size, just from k-mer abundance histogram computed from DNA sequences reads.

Project description

Tool that estimates coverage (and genome size) of dna sequence from reads.

https://badge.fury.io/py/covest.svg https://travis-ci.org/mhozza/covest.svg?branch=master

Installation

pip install covest

For development:

pip install -e . from the project directory

Usage

type covest --help for the usage.

Other included tools

  • geset.py tool for estimation genome size from reads and known coverage

  • prepare_experient.py tool for experiment pipeline setup

  • experiment_table.py tool which collects data from experiment and create a nice table (html, tex, and csv formats are supported)

  • Read simulator:

    • generate_sequence.py random sequence generator

    • read_simulator.py tool for generating random reads form the sequence

Project details


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