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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. Since the enrichment process is imperfect, algorithms are needed to identify putative Y-specific reads prior to downstream assembly.
(Rangavittal et al., 2017) RecoverY: K-mer based read classification for Y-chromosome specific sequencing and assembly. bioRxiv.