srahumanscrubber_initdb

Tags: human database scrubber ncbi download sample-scope

Initialize human read removal database for SRA Human Scrubber.

Uses SRA Human Scrubber to download and initialize the necessary k-mer database required for scrubbing human reads from sequencing data.

Internet Required

This process requires an active internet connection to fetch the database from NCBI FTP.

Outputs

record (
    db: Set<Path>,
    logs: Set<Path?>
)

Field	Type	Description
db	Set<Path>	The initialized SRA Human Scrubber database files
logs	Set<Path?>	Optional program specific log files

Parameters

Used By

Subworkflows

• srahumanscrubber - Remove human contamination from sequencing reads for SRA submission.

Citations

If you use this in your analysis, please cite the following.

• Bactopia
  Petit III RA, Read TD Bactopia - a flexible pipeline for complete analysis of bacterial genomes. mSystems 5 (2020)

• SRA Human Scrubber
  Katz KS, Shutov O, Lapoint R, Kimelman M, Brister JR, and O'Sullivan C STAT: a fast, scalable, MinHash-based k-mer tool to assess Sequence Read Archive next-generation sequence submissions. Genome Biology, 22(1), 270 (2021)

Source

View source on GitHub

Version

SRAHUMANSCRUBBER_INITDB:
    - sra-human-scrubber: 2.2.1