Hi ,

if you have similar samples or multiple metagenomes from the same sampling site, you first need to perform a combined assembly with e.g. Meta Ray and map the reads to the co assembly. After that you can put your bam files and the co assembly  into groupM to extract draft genomes. To check completeness you can pipe the draft genomes to CheckM

http://ecogenomics.github.io/GroopM/

http://ecogenomics.github.io/CheckM/

Hi,

Thanks Mina Bashir . I would perform the steps as told by you. The scenario is pretty much the same as you have described. I hope this will work.

Just a hint: I would use BamM for mapping as it gives you already sorted and indexed bam files. Also all these tools were provided by the same lab so you shouldn't have a compatibility or conversion issue. Good luck 👍🏽