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.
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)
sam_to_fasta.py tool for converting sam file to fasta
Read simulator:
generate_sequence.py random sequence generator
read_simulator.py tool for generating random reads form the sequence
Copyright and citation
Covest is licenced under GNU GPLv3 license.
- Covest is research software, so you should cite us when you use it in scientific publications!
Hozza, M., Vinař, T., & Brejová, B. (2015, September). How Big is that Genome? Estimating Genome Size and Coverage from k-mer Abundance Spectra. In String Processing and Information Retrieval (pp. 199-209). Springer International Publishing.
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