bactopia_qc

Tags: fastq qc adapter-removal error-correction subsampling fastp bbduk lighter porechop nanoq fastqc nanoplot sample-scope

Automated quality control, error correction, and read subsampling.

A comprehensive QC pipeline that adapts to the input read type:

• Illumina: Adapter/PhiX removal (Fastp or BBDuk), Error Correction (Lighter), and Subsampling (Rasusa)
• Nanopore: Adapter removal (Porechop), Quality filtering (Nanoq), and Subsampling (Rasusa)
• Hybrid: Processes both short and long reads through their respective pipelines
• Assembly: Passes through simulated reads from assemblies

Generates quality metrics using fastq-scan and optional quality reports using FastQC (Illumina) and NanoPlot (ONT).

Inputs

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

Field	Type	Description
meta	Record	Groovy Record containing sample information (must include runtype, genome_size, species)
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)
fna	Path?	Assembly file (FASTA) for assembly-based simulations

adapters: Path?
phix: Path?

Name	Type	Description
adapters	Path?	Filepath for custom adapter sequences (FASTA)
phix	Path?	Filepath for custom PhiX sequences (FASTA)

Outputs

record (
    meta: Record,
    r1: Path?,
    r2: Path?,
    se: Path?,
    lr: Path?,
    fna: Path?,
    reads_grouped: Set<Path?>,
    error: Set<Path?>,
    skipped: Path?,
    results: Set<Path>,
    logs: Set<Path?>,
    nf_logs: Set<Path>,
    versions: Set<Path>
)

Field	Type	Description
meta	Record	Sample information record
r1	Path?	QC'd Illumina R1 reads (paired-end forward)
r2	Path?	QC'd Illumina R2 reads (paired-end reverse)
se	Path?	QC'd single-end Illumina reads
lr	Path?	QC'd long reads (ONT)
fna	Path?	Assembly file (FASTA)
reads_grouped	Set<Path?>	All output FASTQs for publishing
error	Set<Path?>	Captured error messages if QC failed (e.g., reads empty after trimming)
skipped	Path?	Marker file indicating QC was skipped for this sample
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

Used By

Subworkflows

• bactopia_qc - Perform comprehensive quality control on sequencing reads.

Workflows

• bactopia - Comprehensive bacterial analysis pipeline for complete genomic characterization.
• cleanyerreads - Quality control and optional host read removal from raw sequencing reads.
• staphopia - Comprehensive analysis pipeline for Staphylococcus aureus isolates.

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)

• BBTools
  Bushnell B BBMap short read aligner, and other bioinformatic tools. (Link)

• fastp
  Chen S, Zhou Y, Chen Y, and Gu J fastp: an ultra-fast all-in-one FASTQ preprocessor. Bioinformatics, 34(17), i884-i890. (2018)

• FastQC
  Andrews S FastQC: a quality control tool for high throughput sequence data. (WebLink)

• fastq-scan
  Petit III RA fastq-scan: generate summary statistics of input FASTQ sequences. (GitHub)

• Lighter
  Song L, Florea L, Langmead B Lighter: Fast and Memory-efficient Sequencing Error Correction without Counting. Genome Biol. 15(11):509 (2014)

• NanoPlot
  De Coster W, D'Hert S, Schultz DT, Cruts M, Van Broeckhoven C NanoPack: visualizing and processing long-read sequencing data Bioinformatics Volume 34, Issue 15 (2018)

• Nanoq
  Steinig E Nanoq: Minimal but speedy quality control for nanopore reads in Rust (GitHub)

• Porechop
  Wick RR, Judd LM, Gorrie CL, Holt KE. Completing bacterial genome assemblies with multiplex MinION sequencing. Microb Genom. 3(10):e000132 (2017)

• Rasusa
  Hall MB Rasusa: Randomly subsample sequencing reads to a specified coverage. (2019).

Source

View source on GitHub

Version

BACTOPIA_QC:
    - bactopia-qc: 1.0.4