Automappa: An interactive interface for metagenome-derived genome bins

Abstract

AbstractBackgroundStudies attempting to observe microbes commonly considered uncultivable under standard laboratory conditions are turning to so-called “deep” environmental sequencing approaches whereby they may access these unculturable organisms’ genomes viain silicoapproaches. A typical workflow involves metagenome assembly, annotation, and binning for reconstruction of each respective organism’s genome (or metagenome-assembled genome, MAG). Many automated genome binning approaches have been developed and have displayed a wide range of variation in performance. Therefore, refinement methods have been developed in order to aid manual curation following the automated genome binning process. Current manual curation tools were developed with a focus towards teaching metagenomics concepts and may fail when handling complex datasets containing many microbes. Automappa was developed with a focus on overlaying a variety of annotations such as taxonomy, coverage and marker-gene prevalence while maintaining an implementation that may scale to the complexity of environmental samples.ResultsWe present Automappa, a companion tool and interactive interface for exploration and refinement of Autometa taxon and genome binning results from metagenomes. Selections provide real-time updates of MAG metrics to aid manual curation. Furthermore, researchers may detect unbinned MAGs as well as manually improve their draft-quality MAGs with contigs that closely match the MAG’s genome characteristics. Automappa’s utility has previously been demonstrated on host-associated, marine and terrestrial systems with a total of 242 curated MAGs across fourteen published metagenomes. Of these refined MAGs, the number of high-quality and medium-quality bins increased, consequently lowering the number of low-quality bins and decreasing the amount of data discarded from downstream analyses. The recovery of higher quality MAGs improved the confidence in results and strengthened the resultant conclusions of these respective studies. Automappa consists of three tabs, one for uploading a user’s metagenome data, another for exploration and refinement and the last for providing an overall summary of the refined MAG results.ConclusionsAutomappa is an open source software package that allows researchers to easily assess and refine undetected or draft-quality MAGs from their respective metagenomes. It is freely available under the GPLv3 license athttps://github.com/WiscEvan/Automappaand through Figshare (doi: 10.6084/m9.figshare.22593235).