sra-human-scrubber¶

Description¶

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.

Environment Modules¶

Run module spider sra_human_scrubber to find out what environment modules are available for this application.

Environment Variables¶

HPC_SRA_HUMAN_SCRUBBER_DIR - installation directory
HPC_SRA_HUMAN_SCRUBBER_BIN - executable directory

Categories¶

genomics