qc_nextflow

A nextflow pipeline for inital QC of Illumina sequencing data from bacteria and viruses

It does the following things:

• Depletion of human-derived reads using Minimap2 to map against Hg38 (though in principle, any fasta sequence could be used)
• Sequencing adaptor and quality trimming using trim_galore
• Estimation of sequencing library insert size using bbmerge
• Summary of trimming and insert size metrics with MultiQC
• Classification of reads using Centrifuge (and a database of choice)
• Plotting of Centrifuge reports using Krona

The pipeline is written in Nextflow, a workflow tool to run tasks across multiple compute infrastructures in a scalable way. It comes with its own docker container.

Dependencies

• Nextflow
• One of Docker, conda or singularity

Usage

You can run it like this:

nextflow run connor-lab/qc_nextflow --fq '/path/to/input_reads/*_R{1,2}.fastq.gz' -profile {docker, singularity, conda}

Help and defaults are available:

nextflow run connor-lab/qc_nextflow --help

Pipeline DAG