Presented at PAGXXV

Altmetric score 26.3 (top 4.2%)

Author: Kevin D Murray
Editor:
Research area: bioinformatics
Type:

Open peer-review

Review content is open, signing review is optional.

kWIP: The k-mer Weighted Inner Product, a de novo Estimator of Genetic Similarity


Created on 4th October 2016

Kevin D Murray; Christfried Webers; Cheng Soon Ong; Justin O Borevitz; Norman Warthmann;


Modern genomics techniques generate overwhelming quantities of data. Extracting population genetic variation demands computationally efficient methods to determine genetic relatedness between individuals or samples in an unbiased manner, preferably de novo. The rapid and unbiased estimation of genetic relatedness has the potential to overcome reference genome bias, to detect mix-ups early, and to verify that biological replicates belong to the same genetic lineage before conclusions are drawn using mislabelled, or misidentified samples. We present the k-mer Weighted Inner Product (kWIP), an assembly-, and alignment-free estimator of genetic similarity. kWIP combines a probabilistic data structure with a novel metric, the weighted inner product (WIP), to efficiently calculate pairwise similarity between sequencing runs from their \k-mer counts. It produces a distance matrix, which can then be further analysed and visualised. Our method does not require prior knowledge of the underlying genomes and applications include detecting sample identity and mix-up, non-obvious genomic variation, and population structure. We show that kWIP can reconstruct the true relatedness between samples from simulated populations. By re-analysing several published datasets we show that our results are consistent with marker-based analyses. kWIP is written in C++, licensed under the GNU GPL, and is available from https://github.com/kdmurray91/kwip.

Show more

Review Summary

This paper has 0 completed reviews and 0 reviews in progress.

# Status Date



Name:
Email: