DiscoverY: a classifier for identifying Y chromosome sequences in male assemblies.

ABSTRACT:

Background

Although the Y chromosome plays an important role in male sex determination and fertility, it is currently understudied due to its haploid and repetitive nature. Methods to isolate Y-specific contigs from a whole-genome assembly broadly fall into two categories. The first involves retrieving Y-contigs using proportion sharing with a female, but such a strategy is prone to false positives in the absence of a high-quality, complete female reference. A second strategy uses the ratio of depth of coverage from male and female reads to select Y-contigs, but such a method requires high-depth sequencing of a female and cannot utilize existing female references.

Results

We develop a k-mer based method called DiscoverY, which combines proportion sharing with female with dep

SUBMITTER: Rangavittal S 

PROVIDER: S-EPMC6688218 | biostudies-literature | 2019 Aug

REPOSITORIES: biostudies-literature