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 ~/workdir/assembly/megahit_out

qsub -cwd -pe multislot 12 -N metabat -l mtc=1 -b y \
/vol/cmg/bin/runMetaBat.sh final.contigs.fa megahit_sorted.bam

MetaBAT will generate 12 bins from our assembly:

final.contigs.fa.metabat-bins-.1.fa
final.contigs.fa.metabat-bins-.2.fa
final.contigs.fa.metabat-bins-.3.fa
final.contigs.fa.metabat-bins-.4.fa
final.contigs.fa.metabat-bins-.5.fa
final.contigs.fa.metabat-bins-.6.fa
final.contigs.fa.metabat-bins-.7.fa
final.contigs.fa.metabat-bins-.8.fa
final.contigs.fa.metabat-bins-.9.fa
final.contigs.fa.metabat-bins-.10.fa
final.contigs.fa.metabat-bins-.11.fa
final.contigs.fa.metabat-bins-.12.fa