Citations

MICOS-2024 gains legitimacy by building on well-established metagenomics and microbiome tools. This page turns that dependency graph into an explicit scholarly trail.

How to cite MICOS-2024 itself

Use the repository citation guidance in CITATION.md, then include tool-specific references when you rely on a given analytical branch.

1. Wood DE, Lu J, Langmead B

   Improved metagenomic analysis with Kraken 2

   Genome Biology · 2019

   Core taxonomic classification reference for the repository taxonomy branch.

   Open source / paper link

2. Bolyen E, Rideout JR, Dillon MR, et al.

   Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2

   Nature Biotechnology · 2019

   Diversity and microbiome interpretation backbone.

   Open source / paper link

3. McIver LJ, Abu-Ali G, Franzosa EA, et al.

   bioBakery: a meta'omic analysis environment

   Bioinformatics · 2018

   Upstream context for KneadData and broader microbiome processing conventions.

   Open source / paper link

4. Franzosa EA, McIver LJ, Rahnavard G, et al.

   Species-level functional profiling of metagenomes and metatranscriptomes

   Nature Methods · 2018

   Functional profiling reference lineage around HUMAnN.

   Open source / paper link

5. McMurdie PJ, Holmes S

   phyloseq: an R package for reproducible interactive analysis and graphics of microbiome census data

   PLoS ONE · 2013

   Important for downstream interpretation and R-facing microbiome workflows.

   Open source / paper link

Why this page matters

For an open-source platform, citation hygiene is part of architectural honesty. It makes clear which pieces were invented here and which pieces were responsibly integrated.