Mapping-free variant calling using haplotype reconstruction from k-mer frequencies.

ABSTRACT:

Motivation

The standard protocol for detecting variation in DNA is to map millions of short sequence reads to a known reference and find loci that differ. While this approach works well, it cannot be applied where the sample contains dense variants or is too distant from known references. De novo assembly or hybrid methods can recover genomic variation, but the cost of computation is often much higher. We developed a novel k-mer algorithm and software implementation, Kestrel, capable of characterizing densely packed SNPs and large indels without mapping, assembly or de Bruijn graphs.

Results

When applied to mosaic penicillin binding protein (PBP) genes in Streptococcus pneumoniae, we found near perfect concordance with assembled contigs at a fraction of the CPU time. Multilo

SUBMITTER: Audano PA 

PROVIDER: S-EPMC5946877 | biostudies-literature | 2018 May

REPOSITORIES: biostudies-literature