deacon_filter

Tags: host contamination decontamination depletion filtering minimizer reads deacon sample-scope

Filter host reads from sequencing data using minimizer-based comparison.

Uses deacon to identify and remove host reads from FASTQ files using SIMD-accelerated minimizer comparison against a pre-built or custom reference index. Supports paired-end, single-end, and long reads.

Database Required

Requires a deacon minimizer index. Use the deacon/fetch module to download a pre-built index (e.g., panhuman-1) or deacon/index to build one from a reference FASTA.

Inputs

record (
    meta: Record,
    r1: Path?,
    r2: Path?,
    se: Path?,
    lr: Path?
)

Field	Type	Description
meta	Record	Groovy Record containing sample information
r1	Path?	Illumina R1 reads (paired-end forward)
r2	Path?	Illumina R2 reads (paired-end reverse)
se	Path?	Single-end Illumina reads
lr	Path?	Long reads (ONT/PacBio)

db: Path

Name	Type	Description
db	Path	Deacon minimizer index file (.idx) for host read filtering

Outputs

record (
    meta: Record,
    special_meta: Record,
    r1: Path?,
    r2: Path?,
    se: Path?,
    lr: Path?,
    scrub_report: Path,
    json_summary: Path,
    results: Set<Path>,
    logs: Set<Path?>,
    nf_logs: Set<Path>,
    versions: Set<Path>
)

Field	Type	Description
meta	Record	Sample information record
special_meta	Record	A simplified metadata record for downstream report joining
r1	Path?	Filtered paired-end forward reads
r2	Path?	Filtered paired-end reverse reads
se	Path?	Filtered single-end reads
lr	Path?	Filtered long reads
scrub_report	Path	Summary report of reads removed during filtering
json_summary	Path	Deacon JSON summary of the filtering run
results	Set<Path>	All output files to be published
logs	Set<Path?>	Optional program specific log files
nf_logs	Set<Path>	Nextflow-specific log files (e.g. .command.{begin
versions	Set<Path>	A YAML formatted file with program versions

Parameters

Deacon Filter Parameters

Parameter	Type	Default	Description
--deacon_abs_threshold	integer	2	Minimum absolute number of minimizer hits for a match
--deacon_db	string		Path to a pre-existing deacon index (.idx) for host read filtering
--deacon_deplete	boolean	true	Discard matching sequences instead of keeping them
--deacon_opts	string		Additional deacon filter options not covered by other parameters
--deacon_prefix_length	integer	0	Search only the first N nucleotides per sequence (0 for all)
--deacon_rel_threshold	number	0.01	Minimum relative proportion (0.0-1.0) of minimizer hits for a match

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_FILTER:
    - bactopia-teton: 1.1.4