nf-core assembly and binning

We will use nf-core/mag (https://nf-co.re/mag) workflow for metagenomics assembly and binning. It starts from reads quality control using fastp, and FastQC. Then:

  • assigns taxonomy to reads using Centrifuge and/or Kraken2

  • performs assembly using MEGAHIT and SPAdes, and checks their quality using Quast

  • (optionally) performs ancient DNA assembly validation using PyDamage and contig consensus sequence recalling with Freebayes and BCFtools

  • predicts protein-coding genes for the assemblies using Prodigal, and bins with Prokka and optionally MetaEuk

  • performs metagenome binning using MetaBAT2, MaxBin2, and/or with CONCOCT, and checks the quality of the genome bins using Busco, or CheckM, and optionally GUNC.

  • Performs ancient DNA validation and repair with pyDamage and Freebayes

  • optionally refines bins with DasTool

  • assigns taxonomy to bins using GTDB-Tk and/or CAT and optionally identifies viruses in assemblies using geNomad, or Eukaryotes with Tiara

  • Before running the workflow, we need to prepare the compressed fastq files as input:

cd /mnt/WGS-data
pigz -k read1.fq
pigz -k read2.fq

  • Then we can start the mag workflow as follows:

cd ..
mkdir -p output_mag
nextflow run nf-core/mag \
  -profile singularity \
  --input 'WGS-data/read{1,2}.fq.gz' \
  --outdir output_mag \
  --skip_concoct \
  --skip_metaeuk \
  --skip_prokka \
  --skip_prodigal \
  --skip_spades \
  --skip_metabat2 \
  --skip_gtdbtk \
  --skip_binqc

In the above command we skipped many software due to limited time and resource. After the pipeline finished, we can view the results stored in the output_mag directory.