Covest estimates the coverage and genome 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.
Requirements
python 3.4+
python3-dev
gcc
Installation
We suggest to install CovEst in python3 virtual environment.
pip install covest
For development:
pip install -e . from the project directory
Usage
type covest --help for the usage.
Basic Usage:
covest histogram -m model -k K -r read_length
You can specify the read file using -s reads.fa parameter for more precise genome size computation.
default K is 21
default read length is 100
currently, the supported models are:
basic: for simple genomes without repeats
repeat: for genomes with repetitive sequences
Input Histogram Specification:
The input histogram can be generated from the read data using jellyfish.
jellyfish count -m K -C reads.fa -o table.jf
jellyfish histo table.jf -o reads.hist
The format of the histogram is just list of lines. Each lines contains an index and value separated by space.
Output Specification:
CovEst outputs it’s results in simple subset of YAML format for best human readability and possibility of machine processing.
The output are lines containing key: value. The most important keys are coverage and genome_size (or genome_size_reads if read file was specified).
Other included tools
geset.py tool for estimation genome size from reads and known coverage
kmer_hist.py custom khmer histogram computation, it is much slower than other tools, so use it only if you have no other option.
read_sampler.py script for subsampling reads, useful if you have very high coverage data and want to make it smaller.
fasta_length.py get total length of all sequences in fasta file.
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.
Release history Release notifications | RSS feed
Download files
Download the file for your platform. If you're not sure which to choose, learn more about installing packages.
Source Distribution
File details
Details for the file covest-0.4.3.tar.gz.
File metadata
- Download URL: covest-0.4.3.tar.gz
- Upload date:
- Size: 38.0 kB
- Tags: Source
- Uploaded using Trusted Publishing? No
File hashes
| Algorithm | Hash digest | |
|---|---|---|
| SHA256 | 489c34aaba3409d329d2af51a00eb36518443914465b96392d652674bf05b25d |
|
| MD5 | adc3f3957332400b519fbe0e3261aa6f |
|
| BLAKE2b-256 | 58618c765f626807a68779c036fcaa6549e014bdc01d731ed2a20902b0d70286 |
