MaxBin Binning

MaxBin is a software that is capable of clustering metagenomic contigs into different bins, each consists of contigs from one species. MaxBin uses the nucleotide composition information and contig abundance information to do achieve binning through an Expectation-Maximization algorithm. For users’ convenience MaxBin will report genome-related statistics, including estimated completeness, GC content and genome size in the binning summary page. See the MaxBin home page for more info.

Let’s run a MaxBin binning on the MEGAHIT assembly. First, we need to generate an abundance file from the mappes reads:

cd ~/workdir/assembly/megahit_out
pileup.sh in=megahit.sam  out=cov.txt
awk '{print $1"\t"$5}' cov.txt | grep -v '^#' > abundance.txt

Next, we can run MaxBin:

qsub -cwd -pe multislot 24 -N maxbin -l mtc=1 -b y \
/vol/cmg/lib/MaxBin-2.1.1/run_MaxBin.pl -thread 24 -contig final.contigs.fa -out maxbin -abund abundance.txt

Assume your output file prefix is (out). MaxBin will generate information using this file header as follows.

(out).0XX.fasta	the XX bin. XX are numbers, e.g. out.001.fasta
(out).summary	summary file describing which contigs are being classified into which bin.
(out).log	log file recording the core steps of MaxBin algorithm
(out).marker	marker gene presence numbers for each bin. This table is ready to be plotted by R or other 3rd-party software.
(out).marker.pdf	visualization of the marker gene presence numbers using R
(out).noclass	all sequences that pass the minimum length threshold but are not classified successfully.
(out).tooshort	all sequences that do not meet the minimum length threshold.

Now you can run a gene prediction on each genome bin and BLAST one sequence for each bin for a (very crude!) classification:

for i in max*fasta; do prodigal -p meta -a $i.genes.faa -d $i.genes.fna -f gff -o $i.genes.gff -i $i& done

Does the abundance of the bins match the 16S profile of the community?