Whole metagenome analysis with MOSHPIT
Welcome! 👋 MOSHPIT (MOdular SHotgun metagenome Pipelines with Integrated provenance Tracking) is a toolkit of plugins for whole metagenome assembly, annotation, and analysis built on the microbiome multi-omics data science framework QIIME 2. MOSHPIT enables flexible, modular, fully reproducible workflows for read-based or assembly-based analysis of metagenome data.
Figure 1:Schematic of current analysis workflows available in MOSHPIT.
The following main plugins comprise the core of the MOSHPIT toolkit and are included in the MOSHPIT distribution:
q2-assembly
This plugin contains actions for (meta)genome assembly and quality control, genome indexing and red mapping.
q2-annotate
This plugin provides actions for contig binning and quality control, taxonomic and functional annotations of contigs and MAGs, human host removal.
q2-fastp
This plugin provides actions for quality control using fastp.
q2-sourmash
This plugin provides actions for computing and comparing MinHash signatures using sourmash.
q2-fondue
This plugin provides actions for data retrieval from SRA.
You may also want to check out these other QIIME 2 plugins for antimicrobial resistance gene (ARG) detection and viromics applications. These plugins are not covered in this tutorial. They have their own installation instructions and tutorials (see the wiki page on the respective GitHub repositories). You can use these plugins with some of the artifacts produced by q2-assembly and q2-annotate:
q2-rgi
q2-amrfinderplus
ARG detection using the AMRFinderPlus tool.
q2-viromics
Detection of viral sequences and their quality control.
Finally, here are some other plugins we developed and that are compatible with metagenomic workflows: