deacon
Tags: host contamination decontamination depletion filtering minimizer reads deacon sample-scope
Remove host reads from sequencing data using deacon.
This subworkflow uses deacon to identify and remove host reads from FASTQ files using SIMD-accelerated minimizer comparison against a pre-built reference index (default: panhuman-1). It optionally downloads the index if not already available.
Take
reads: Channel<Record>
| Field | Description |
|---|---|
meta | Groovy Record containing sample information |
r1 | Illumina R1 reads (paired-end forward) |
r2 | Illumina R2 reads (paired-end reverse) |
se | Single-end Illumina reads |
lr | Long reads (ONT/PacBio) |
database: Path?
download_deacon: Boolean
| Name | Type | Description |
|---|---|---|
database | Path? | Path to deacon minimizer index file (.idx) (ignored if download_deacon is true) |
download_deacon | Boolean | Boolean flag to download the index instead of using the provided path |
Emit
Published
The sample_outputs and run_outputs emissions are aggregates of output files that will be published in the entry workflow.
sample_outputs
| Output | Description |
|---|---|
special_meta | Simplified metadata record for downstream report joining |
r1 | Filtered paired-end forward reads |
r2 | Filtered paired-end reverse reads |
se | Filtered single-end reads |
lr | Filtered long reads |
scrub_report | Read filtering statistics report |
run_outputs
No run-scope outputs.
Module Composition
This subworkflow calls the following modules:
- deacon_fetch - Fetch a pre-built deacon index for host read filtering.
- deacon_filter - Filter host reads from sequencing data using minimizer-based comparison.
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)