View source for Sra-human-scrubber

[[Category:Software]][[Category:Genomics]]
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|{{#vardefine:app|sra-human-scrubber}}
|{{#vardefine:url|https://github.com/ncbi/sra-human-scrubber}}
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The human read removal tool (HRRT) is based on the SRA Taxonomy Analysis Tool that will take as input a fastq file, and produce as output a fastq.clean file in which all reads identified as potentially of human origin are removed. The HRRT is based on a k-mer database that is constructed from the k-mers derived from all human RefSeq records and subtracts the library of k-mers generated from all non-Eukaryota RefSeq records. The remaining set of k-mers are the database used to ID human reads by the removal tool. This means it tends to be aggressive about identifying human reads since it contains not only human-specific k-mers, but also k-mers common to primates, mammals, and other lineages further up the Eukaryotic tree. However, it is also fairly conservative at maintaining any viral or bacterial clinical pathogen sequences. It takes a fastq file as input, removes any reads with hits to the human k-mer database and outputs a fastq.clean with the identified human reads removed.

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