MetaBAT Binning

MetaBAT, An Efficient Tool for Accurately Reconstructing Single Genomes from Complex Microbial Communities.

Grouping large genomic fragments assembled from shotgun metagenomic sequences to deconvolute complex microbial communities, or metagenome binning, enables the study of individual organisms and their interactions. MetaBAT is an automated metagenome binning software which integrates empirical probabilistic distances of genome abundance and tetranucleotide frequency. See the MetaBAT home page for more info.

Let’s run a MetaBAT binning on the MEGAHIT assembly:

cd /vol/spool/workdir/assembly/megahit_out
mkdir metabat
cd metabat

qsub -cwd -pe multislot 14 -N metabat -b y \
/usr/bin/runMetaBat.sh ../final.contigs.fa ../megahit_sorted.bam

MetaBAT will generate 12 bins from our assembly:

ls final.contigs.fa.metabat-bins

bin.1.fa
bin.2.fa
bin.3.fa
bin.4.fa
bin.5.fa
bin.6.fa
bin.7.fa
bin.8.fa
bin.9.fa
bin.10.fa
bin.11.fa
bin.12.fa