srahumanscrubber_scrub

Tags: human contamination scrubber decontamination ncbi sra sample-scope

Scrub human reads from FASTQ files.

Uses SRA Human Scrubber to identify and remove human reads from sequencing data. It relies on a specific k-mer database to mask or remove sequences that align to human references.

Uses explicit positional named parameters for reads:

• Input: record(meta, r1, r2, se, lr) where each read slot is Path?

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)
r2	Path?	Illumina R2 reads (paired-end)
se	Path?	Single-end Illumina reads
lr	Path?	Long reads (ONT/PacBio)

db: Path

Name	Type	Description
db	Path	SRA Human Scrubber database directory

Outputs

record (
    meta: Record,
    special_meta: Record,
    r1: Path?,
    r2: Path?,
    se: Path?,
    lr: Path?,
    scrub_report: 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?	Scrubbed paired-end forward reads
r2	Path?	Scrubbed paired-end reverse reads
se	Path?	Scrubbed single-end reads
lr	Path?	Scrubbed long reads
scrub_report	Path?	Report of scrubbing statistics
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

SRA Human Scrubber Parameters

Parameter	Type	Default	Description
--use_srascrubber	boolean	false	Use SRAHumanScrubber for scrubbing human reads

Used By

Subworkflows

• srahumanscrubber - Remove human contamination from sequencing reads for SRA submission.

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)

• SRA Human Scrubber
  Katz KS, Shutov O, Lapoint R, Kimelman M, Brister JR, and O'Sullivan C STAT: a fast, scalable, MinHash-based k-mer tool to assess Sequence Read Archive next-generation sequence submissions. Genome Biology, 22(1), 270 (2021)

Source

View source on GitHub

Version

SRAHUMANSCRUBBER_SCRUB:
    - bactopia-teton: 1.1.3