deacon_fetch

Tags: host decontamination depletion download index minimizer deacon run-scope

Fetch a pre-built deacon index for host read filtering.

Uses deacon to download a pre-built minimizer index for filtering host reads from sequencing data. The default index is panhuman-1, which covers human reference genomes for human read depletion.

Internet Required

This process requires an active internet connection to fetch the pre-built index.

Outputs

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

Field	Type	Description
db	Path	The pre-built deacon minimizer index file
logs	Set<Path?>	Optional program specific log files

Parameters

Deacon Fetch Parameters

Parameter	Type	Default	Description
--deacon_index_name	string	panhuman-1	Name of the pre-built deacon index to fetch
--download_deacon	boolean	false	Download the deacon index to the datasets cache
--use_deacon	boolean	false	Use deacon for host read filtering

Used By

Subworkflows

• deacon - Remove host reads from sequencing data using deacon.

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)

• deacon
  Bede N. deacon: SIMD-accelerated filtering of DNA sequences using minimizer-based comparison. (GitHub)

Source

View source on GitHub

Version

DEACON_FETCH:
    - bactopia-teton: 1.1.4