deacon_index

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

Build a deacon minimizer index from a FASTA reference genome.

Uses deacon to build a minimizer index from a reference genome in FASTA format. The resulting index is used by the deacon filter module to remove host contamination from sequencing reads via SIMD-accelerated minimizer comparison.

Build Once

This process builds a minimizer index from a reference FASTA. The index is cached via storeDir and only needs to be built once per reference genome.

Inputs

reference: Path

Name	Type	Description
reference	Path	Reference genome in FASTA format to build the minimizer index from

Outputs

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

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

Parameters

Deacon Index Parameters

Parameter	Type	Default	Description
--deacon_reference	string		Path to a reference genome FASTA file to build the deacon index from

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_INDEX:
    - bactopia-teton: 1.1.4