nohuman_download

Tags: bacteria database download human decontamination kraken2 nohuman run-scope

Download the nohuman database for human read removal.

Fetches the Kraken2-based database used by nohuman to classify and remove human reads from sequencing datasets. The database is built from Human Pangenome Reference Consortium (HPRC) genomes.

Internet & Storage Required

This process requires an active internet connection and sufficient disk space to store the Kraken2 database files.

Outputs

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

Field	Type	Description
db	Path?	The nohuman Kraken2 database directory
db_tarball	Path?	A compressed tarball of the database (if requested via parameters)
logs	Set<Path?>	Optional program specific log files

Parameters

Nohuman Download Parameters

Parameter	Type	Default	Description
--nohuman_db	string		Path to the nohuman database or directory to download it to
--nohuman_db_version	string		Database version to download (default: latest HPRC release)
--nohuman_save_as_tarball	boolean	false	Save the nohuman database as a tarball
--download_nohuman	boolean	false	Download the nohuman database to the path given by --nohuman_db

Used By

Subworkflows

• nohuman - Remove human reads from sequencing data using nohuman.

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)

• Kraken2
  Wood DE, Lu J, Langmead B Improved metagenomic analysis with Kraken 2. Genome Biology, 20(1), 257. (2019)

Source

View source on GitHub

Version

NOHUMAN_DOWNLOAD:
    - bactopia-teton: 1.1.3