indrikwijaya/nf-mgx-short is a bioinformatics pipeline that takes raw metagenomic (short reads) (MGX) and annotates them at the taxonomic, functional and resistome levels.

The pipeline is built using Nextflow DSL2 , a workflow tool to run tasks across multiple compute infrastructures in a very portable manner. It uses Docker containers (also compatible with Singularity) for ease of installation and computational reproducibility.

This pipeline currently only accepts paired-end reads as inputs.

1. Adapter trimming and quality control using fastp (0.22.0)

2. Removal of host (human) reads by mapping to a reference genome using bwa (0.7.17)

3. Taxonomic classification of non-human reads

   a. using Kraken2 (2.1.2) and taxonomic abundance re-estimation using Bracken (2.6.1)

   b. using Metaphlan4 (4.0.6)

4. Functional annotation of reads using HUMANN3

5. Resistome annotation of reads using SRST2

1. Install Nextflow (>=21.04.0) and add the nextflow executable to your $PATH

2. Install Docker

3. Clone the pipeline and refer to the help message

   $ git clone https://github.com/indrikwijaya/nf-mgx-short
   
   $ nextflow run ./nf-mgx-short/main.nf --help

• Add a custom config file which contains the paths to various pre-installed databases. Refer to the test.config file in this repo for an example.
• Add a custom profile in the nextflow.config file, allowing you to specify the use of docker or singularity, and/or a task scheduler.

4. Make sure all helper scripts in nf-mgx-short/bin have execute permissions

   $ cd bin/
   $ chmod +x ./nf-mgx-short/bin/*

5. Run the pipeline

   $ nextflow run ./nf-mgx-short/main.nf -profile docker,your_profile --profilers metaphlan4 --read_path /path/to/metagenomes --outdir /path/to/results

• You can specifiy multiple profiles separated by comma, e.g. -profile docker,sge.
• The taxonomic classification, nucleotide alignment, translated search and annotation modules can be quite memory intensive depending on the databases used
• Delete the work/ directory after running the pipeline to free up space taken up by intermediate files

Contact: Indrik Wijaya [email protected], [email protected]