Dataset Information
RecoverY: k-mer-based read classification for Y-chromosome-specific sequencing and assembly.
Ontology highlight
ABSTRACT: Motivation
The haploid mammalian Y chromosome is usually under-represented in genome assemblies due to high repeat content and low depth due to its haploid nature. One strategy to ameliorate the low coverage of Y sequences is to experimentally enrich Y-specific material before assembly. As the enrichment process is imperfect, algorithms are needed to identify putative Y-specific reads prior to downstream assembly. A strategy that uses k-mer abundances to identify such reads was used to assemble the gorilla Y. However, the strategy required the manual setting of key parameters, a time-consuming process leading to sub-optimal assemblies.Results
We develop a method, RecoverY, that selects Y-specific reads by automatically choosing the abundance level at which a k-mer is deemed to originate from the Y. This algorithm uses prior knowledge about the Y chromosome of a related species or known Y transcript sequences. We evaluate RecoverY on both simulated and real data, for human and gorilla, and investigate its robustness to important parameters. We show that RecoverY leads to a vastly superior assembly compared to alternate strategies of filtering the reads or contigs. Compared to the preliminary strategy used by Tomaszkiewicz et al., we achieve a 33% improvement in assembly size and a 20% improvement in the NG50, demonstrating the power of automatic parameter selection.Availability and implementation
Our tool RecoverY is freely available at https://github.com/makovalab-psu/RecoverY.Contact
kmakova@bx.psu.edu or pashadag@cse.psu.edu.Supplementary information
Supplementary data are available at Bioinformatics online.
SUBMITTER: Rangavittal S
PROVIDER: S-EPMC6030959 | biostudies-literature | 2018 Apr
REPOSITORIES: biostudies-literature
Publications
RecoverY: k-mer-based read classification for Y-chromosome-specific sequencing and assembly.
Bioinformatics (Oxford, England) 20180401 7
<h4>Motivation</h4>The haploid mammalian Y chromosome is usually under-represented in genome assemblies due to high repeat content and low depth due to its haploid nature. One strategy to ameliorate the low coverage of Y sequences is to experimentally enrich Y-specific material before assembly. As the enrichment process is imperfect, algorithms are needed to identify putative Y-specific reads prior to downstream assembly. A strategy that uses k-mer abundances to identify such reads was used to a ...[more]