diff --git a/moshpit_docs/intro.md b/moshpit_docs/intro.md index b78b11d..e32af52 100644 --- a/moshpit_docs/intro.md +++ b/moshpit_docs/intro.md @@ -5,6 +5,19 @@ metagenome assembly and analysis as part of the microbiome multi-omics data scie MOSHPIT enables flexible, modular, fully reproducible workflows for read-based or assembly-based analysis of metagenome data. +The following main plugins comprise the core of the MOSHPIT suite: +- [q2-assembly](https://github.com/bokulich-lab/q2-assembly): contains actions for (meta)genome and quality control, + genome indexing and red mapping +- [q2-moshpit](https://github.com/bokulich-lab/q2-moshpit): provides actions for contig binning and quality control, + taxonomic and functional annotations of contigs and MAGs, human host removal. + +Additionally, you may want to check out our plugins for AMR genes detection and viromics applications (they are not +covered in this tutorial but you may use them with some of the artifacts produced by the MOSHPIT plugins): +- [q2-rgi](https://github.com/bokulich-lab/q2-rgi): antimicrobial resistance gene annotation of MAGs and metagenomic + reads with RGI and CARD +- [q2-amrfinderplus](https://github.com/bokulich-lab/q2-amrfinderplus): AMR detection using the AMRFinderPlus tool +- [q2-viromics](https://github.com/bokulich-lab/q2-viromics): detection of viral sequences and their quality control. + This tutorial will guide you through the process of analyzing metagenomic data using QIIME 2 framework and MOSHPIT. The tutorial is divided into several chapters, each focusing on a different aspect of metagenomic data analysis. We will use a small published dataset to demonstrate the capabilities of most of the methods available in MOSHPIT.