SRA-Human-Scrubber
Description
SRA-Human-Scrubber website
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.
System Variables
- HPC_SRA_HUMAN_SCRUBBER_DIR - installation directory
- HPC_SRA_HUMAN_SCRUBBER_BIN - executable directory
- HPC_SRA_HUMAN_SCRUBBER_SCR - Scripts directory
Job Script Examples
See the SRA-Human-Scrubber_Job_Scripts page for SRA-Human-Scrubber Job script examples.