v-met

A bare-bones, ridiculously simple metagenomics pipeline for viruses using Kraken 2 written in Nextflow.

This project follows the semver pro forma and uses the git-flow branching model.

Installation

1. Install Nextflow (>= 21.10.6)
2. Install [Conda]
3. Install one or more of
   • Singularity (Recommended)
   • Podman
   • Docker
4. Download a Kraken2 database
5. Download a BLAST database

Check out the Installation docs for a more nuanced take on the requirements.

Usage

Syntax

nextflow run ksumngs/v-met               \
  -profile <singularity,podman,docker>   \
  --platform <illumina,nanopore>         \
  --kraken2_db /path/to/kraken2/database \
  --blast_db /path/to/blast/database     \
  [--input /path/to/reads/folder]        \
  [--blast_target list]                  \
  [--outdir /path/to/output]

Example: Illumina reads with a relatively complete Kraken2 database

nextflow run ksumngs/v-met          \
  -profile singularity               \
  --platform illumina                \
  --kraken2_db /databases/kraken2/nt \
  --blast_target 'none'

Example: Nanopore reads with a viral-only Kraken2 database

nextflow run ksumngs/v-met             \
  -profile podman                       \
  --platform nanopore                   \
  --kraken2_db /databases/kraken2/viral \
  --blast_db /databases/blast/          \
  --blast_target classified

There are way more parameters than listed here. For a more complete description, please read the docs on Usage and Parameters.