RecoverY: k-mer-based read classification for Y-chromosome-specific sequencing and assembly

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.