Chapter 24 MetaBAT2

We will use MetaBAT2 for genome binning. It has three major upsides that makes it very popular:

  1. It has very reliable default parameters meaning virtually no parameter optimisation is required.
  2. It performs very well amongst genome binners.
  3. It is computationally efficient compared to other binners (requires less RAM, cores etc.).

Make a new directory and move into it.

#Make directory
mkdir -p ~/7-Binning/K1
#Move into it
cd ~/7-Binning/K1

24.1 MetaBAT2

With our assembly and its depth information we can run MetaBAT2 for binning.

#make a diretcory for the bins
mkdir bins
#Run MetaBAT2
metabat2 \
--inFile ~/6-Assembly/K1/final.contigs.fa \
--outFile bins/K1 \
--abdFile ~/6-Assembly/K1.depth.txt \
--minContig 1500

Parameters

  • --inFile: Input metagenome assembly fasta file.
  • --outFile: Prefix of output files.
  • --abdFile: Contig depth file.
  • --minContig: Minimum size of contigs to be used for binning.
    • The default is 2500.
    • We used the minimum value of 1500 as we are using tutorial data. We recommend using the default in your own analysis.

24.2 Bins

List the contents of the output directory and you'll see there is 1 fasta file with the prefix of K1. This is a bin that will hopefully contain 1 MAG. In your future analysis you may get many bins, each hopefully containing only one MAG.

ls bins

Super! In the next chapter we will assess the quality of these bins.