MetaBAT2 (Binning)

Upload the final_contigs_file from MEGAHIT to Galaxy MetaBAT2: https://usegalaxy.eu/?tool_id=toolshed.g2.bx.psu.edu/repos/iuc/metabat2/metabat2/2.15+galaxy1

Or install MetaBAT2 via conda:

conda install -c bioconda/label/cf201901::metabat2

Generate contig depth and run MetaBAT2:

jgi_summarize_bam_contig_depths --outputDepth depth.txt *.bam
metabat2 -i final.contigs.fa -a depth.txt -o bins_dir/bin