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• Getting started
• Workflow outline

Getting started

From GitHub

To start using the workflow either clone the latest version of the repo:

git clone https://github.com/NBISweden/nbis-meta.git

or download the latest release from the release page and extract the archive.

Then change directory into the nbis-meta folder and create the core conda environment:

cd nbis-meta
conda env create -f environment.yml

From DockerHub

You may also pull the latest Docker image:

docker pull nbisweden/nbis-meta:2.2

to get version 2.2.

What's next?

You are now ready to start using the workflow! Check out the How-to page, see how to create a sample list to start working with your own data or delve into the configuration parameters.

Workflow outline

1. Preprocessing

This workflow can perform preprocessing of paired- and/or single-end whole-genome shotgun metagenomic data (in fastq-format) using e.g.:

• Trimmomatic (adapter/quality trimming)
• Cutadapt (adapter trimming)
• SortMeRNA (rRNA filtering)
• Fastuniq (de-duplication)
• FastQC and MultiQC (read QC and report generation)

2a. Read-based classification

Preprocessed reads can be used for taxonomic classification and profiling using tools such as:

• Kraken2
• Centrifuge
• MetaPhlAn3

producing taxonomic profiles of the samples, as well as interactive krona plots.

2b. Assembly-based analysis

Preprocessed reads can also be assembled and analyzed further using tools such as:

• Megahit/MetaSPADES (for metagenomic assembly)
• prodigal (gene calling)
• pfam_scan, eggnog-mapper, Resistance Gene Identifier (protein level annotations)
• bowtie2 (mapping reads to contigs)
• featureCounts (assigning and counting mapped reads)
• edgeR + metagenomeSEQ (normalization of read counts for genes/features)
• contigtax + sourmash (taxonomic assignments)
• metabat2, CONCOCT, MaxBin2 (metagenomic binning)
• checkm (genome bin QC)
• GTDB-TK (genome bin phylogenetic assignments)
• fastANI (genome bin clustering)

TEST