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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.


Sequence assembly


  • Operation: Sequence assembly; De novo assembly
  • Input: FASTQ
  • Output: -
  • Software interface: Command-line user interface
  • Language: Python
  • Operating system: Linux; Mac OS X
  • License: The MIT licence
  • Cost: Free
  • Version name: -
  • Credit: National Science Foundation
  • Contact: kmakova _at_;pashadag _at_
  • Collection: -


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.
PMID: 29194476
PMCID: PMC6030959

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