MAGs generation pipeline

MGnify genomes generation pipeline to generate prokaryotic and eukaryotic MAGs from reads and assemblies.

This pipeline does not support co-binning.

Pipeline summary

The pipeline performs the following tasks:

• Supports short reads.
• Changes read headers to their corresponding assembly accessions (in the ERZ namespace).
• Quality trims the reads, removes adapters fastp.

Afterward, the pipeline:

• Runs a decontamination step using BWA to remove any host reads. By default, it uses the hg39.fna.
• Bins the contigs using Concoct, MetaBAT2 and MaxBin2.
• Refines the bins using the metaWRAP bin_refinement compatible subworkflow supported separately.

For prokaryotes:

• Conducts bin quality control with CAT, GUNC, and CheckM.
• Performs dereplication with dRep.
• Calculates coverage using MetaBAT2 calculated depths.
• Detects rRNA and tRNA using cmsearch.
• Assigns taxonomy with GTDBtk.

For eukaryotes:

• Estimates quality and merges bins using EukCC.
• Dereplicates MAGs using dRep.
• Calculates coverage using MetaBAT2 calculated depths.
• Assesses quality with BUSCO and EukCC.
• Assigns taxonomy with BAT.

Final steps:

• Tools versions are available in software_versions.yml
• Pipeline generates a tsv table for public MAG uploader
• TODO: finish MultiQC

Usage

If this the first time running nextflow please refer to this page

Required reference databases

You need to download the mentioned databases and add them to config/dbs.config.

Don't forget to add this configuration to the main .nextflow.config.

• BUSCO
• CAT
• CheckM
• EukCC
• GUNC
• GTDB-Tk + ar53_metadata_r214.tsv, bac120_metadata_r214.tsv from here
• Rfam
• The reference genome of your choice for decontamination, as a .fasta.

Citation

If you use this pipeline please make sure to cite all used software.