aweMAGs: a fully automated workflow for quality assessment and annotation of eukaryotic genomes from metagenomes

Abstract

Metagenomics is one of the most promising approaches to identify and characterize novel microbial species from environmental samples. While a large amount of prokaryotic metagenome assembled genomes (MAGs) have been published, only a few examples of eukaryotic MAGs have been reported. This is in part due to the absence of dedicated and easy-to-use processing pipelines. Quality assessment, annotation and phylogenomic placement of eukaryotic MAGs involve the use of several computational tools and reference databases that are often difficult to collect and maintain. We present metashot/aweMAGs, a fully automated workflow capable of performing all these steps. metashot/aweMAGs can run out-of-the-box on any platform that supports Docker, Singularity and Nextflow, including computing clusters or batch systems in the cloud.