Identifying, understanding, and correcting technical artifacts on the sex chromosomes in next-generation sequencing data.

ABSTRACT:

Background

Mammalian X and Y chromosomes share a common evolutionary origin and retain regions of high sequence similarity. Similar sequence content can confound the mapping of short next-generation sequencing reads to a reference genome. It is therefore possible that the presence of both sex chromosomes in a reference genome can cause technical artifacts in genomic data and affect downstream analyses and applications. Understanding this problem is critical for medical genomics and population genomic inference.

Results

Here, we characterize how sequence homology can affect analyses on the sex chromosomes and present XYalign, a new tool that (1) facilitates the inference of sex chromosome complement from next-generation sequencing data; (2) corrects erroneous read mapping on

SUBMITTER: Webster TH 

PROVIDER: S-EPMC6615978 | biostudies-literature | 2019 Jul

REPOSITORIES: biostudies-literature