MOSHPIT: Decoding functions of microbial communities using reproducible shotgun metagenomics with provenance tracking in QIIME 2

Shotgun metagenome sequencing is an untargeted high-throughput DNA sequencing approach that enables detection and characterization of all microbial genomes present in a given sample. It can be used to recover whole genome sequences of both known and unknown microbial species. Additionally, it allows taxonomic profiling of microbial communities, as well as determination of their functional potential. The multitude of analysis tools, the absence of standardized workflows and lacking systematic provenance tracking complicate the analysis process, particularly for newcomers to metagenomics. Here, we present MOSHPIT (Modular Shotgun metagenome Pipelines with Integrated provenance Tracking), a suite of QIIME 2 plugins designed to streamline every stage of shotgun metagenomic analysis and guarantee exceptional traceability and reproducibility of the workflows and accommodating researchers at different expertise levels.