RecoverY is a tool for identifying Y chromosome specific reads for assembly of the Y chromosome. The approach is based on k-mer abundance of reads and uses knowledge of known Y chromosome sequences from related species or transcripts. The results of this tool on assembling human and gorilla Y chromosomes were given and users may try the approach for other species Y chromosomes.
Rangavittal S, Harris RS, Cechova M, Tomaszkiewicz M, Chikhi R, Makova KD, Medvedev P "RecoverY: k-mer-based read classification for Y-chromosome-specific sequencing and assembly." Bioinformatics. 2018 Apr 1;34(7):1125-1131. https://doi.org/10.1093/bioinformatics/btx771
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