https://github.com/kdm9/kwip

De novo estimates of genetic relatedness from next-gen sequencing data
https://github.com/kdm9/kwip

Last synced: 19 days ago
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De novo estimates of genetic relatedness from next-gen sequencing data

• Host: GitHub
• URL: https://github.com/kdm9/kwip
• Owner: kdm9
• License: gpl-3.0
• Created: 2015-03-23T03:43:20.000Z (over 9 years ago)
• Default Branch: master
• Last Pushed: 2019-07-28T13:14:47.000Z (over 5 years ago)
• Last Synced: 2024-10-11T19:22:40.726Z (about 1 month ago)
• Language: C++
• Homepage: https://kwip.readthedocs.org
• Size: 3.82 MB
• Stars: 45
• Watchers: 10
• Forks: 3
• Open Issues: 0
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

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README

        
kWIP

====

The k-mer Weighted Inner Product.

This software implements a *de novo*, *alignment free* measure of sample

genetic dissimilarity which operates upon raw sequencing reads. It is able to

calculate the genetic dissimilarity between samples without any reference

genome, and without assembling one.

[![Build Status](https://travis-ci.org/kdmurray91/kWIP.svg?branch=master)](https://travis-ci.org/kdmurray91/kWIP)

[![gplv3+](https://img.shields.io/badge/license-GPLv3-blue.svg)](https://www.gnu.org/licenses/gpl.html)

[![Documentation Status](https://readthedocs.org/projects/kwip/badge/?version=latest)](https://kwip.readthedocs.org)

Full documentation is available at https://kwip.readthedocs.org

Installation

============

See the [``kWIP``

Documentation](http://kwip.readthedocs.org/en/latest/installation.html)

How it works

============

kWIP works by decomposing sequencing reads to short

[k-mers](https://en.wikipedia.org/wiki/K-mer),

[hashing](https://en.wikipedia.org/wiki/Hash_function) these k-mers and

performing pairwise distance calculation between these sample k-mer hashes. We

use [`khmer`](https://github.com/dib-lab/khmer) from the DIB lab, UC Davis to

hash sequencing reads. `KWIP` calculates the distance between samples in a

computationally efficient manner, and generates a distance matrix which may be

used by downstream tools. The power of `kWIP` comes from the weighting applied

across different hash values, which decreases the effect of erroneous, rare or

over-abundant k-mers while focusing on k-mers which give the most insight into

the similarity of samples.

License

=======

kWIP is Copyright 2015 Kevin Murray, and released under the GNU General Public

License version 3 (or any later version).

Publication

===========

A publication describing kWIP has been [published in PLOS Computational Biology](https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1005727)