Tools and Technology

Software and online resources used by, or developed as part of the iHMP are provided here. We are continuing to add tools as they become available.

Metaviz is a tool for interactive visualization and exploration of metagenomic sequencing data. Metaviz provides a novel navigation tool for exploring hierarchical feature data that is coupled with multiple data visualizations including heatmaps, stacked bar charts, and scatter plots.
Quantitative Insight Into Microbial Ecology: QIIME is an open-source 16S bioinformatics pipeline designed to take users from raw sequencing data through publication quality graphics and statistics. This includes demultiplexing and quality filtering, OTU picking, taxonomic assignment, and phylogenetic reconstruction, and diversity analyses and visualizations.
NCBI's Best Match Tagger for removing human reads from metagenomics datasets. All HMP metagenomic sequence submitted to NCBI's Sequence Read Archive is being human filtered using BMTagger.
HUMAnN is a pipeline for efficiently and accurately profiling the presence/absence and abundance of microbial pathways in a community from metagenomic or metatranscriptomic sequencing data (typically millions of short DNA/RNA reads). This process, referred to as functional profiling, aims to describe the metabolic potential of a microbial community and its members.
Qiita is an entirely open-source microbial study management platform. It allows users to keep track of multiple studies with multiple ‘omics data. Additionally, Qiita is capable of supporting multiple analytical pipelines through a 3rd-party plugin system, allowing the user to have a single entry point for all their analyses.
AnaDAMA2 is a tool to create reproducible workflows and execute them efficiently. Essential information from all tasks is recorded to ensure reproducibility. An auto-doc feature allows for workflows to generate documentation automatically to further ensure reproducibility by capturing the latest essential workflow information. AnADAMA2 was architected to be modular, and has been used by the iHMP consortium for data processing and deposition of data to public repositories.
An iHMP domain specific API using osdf-python
Centralized access to Dockerized tools and pipelines for metagenomics developed by the Human Microbiome Project members. Initially developed for the HMP Cloud Workshop, you can run common metagenomics tools on the command line interactively within Docker or run entire pipelines at once.
Framework for submitting proteomics data to the PRIDE archive at EBI
MetaPhlAn is a computational tool for profiling the composition of microbial communities (Bacteria, Archaea, Eukaryotes and Viruses) from metagenomic shotgun sequencing data with species level resolution. From version 2.0, MetaPhlAn is also able to identify specific strains (in the not-so-frequent cases in which the sample contains a previously sequenced strains) and to track strains across samples for all species.
StrainPhlAn is a tool for strain-level resolution of species across large sample sets, based on single nucleotide polymorphisms (SNPs) within conserved and unique species marker genes.
PanPhlAn is a strain-level metagenomic profiling tool for identifying the gene composition and in-vivo transcriptional activity of individual strains in metagenomic samples. PanPhlAn’s ability for strain-tracking and functional analysis of unknown pathogens makes it an efficient tool for culture-free infectious outbreak epidemiology and microbial population studies.
GraPhlAn is a software tool for producing high-quality circular representations of taxonomic and phylogenetic trees. GraPhlAn focuses on concise, integrative, informative, and publication-ready representations of phylogenetically- and taxonomically-driven investigation.

Shared protocols used by, or developed as part of the iHMP will be provided here as they become available.
Please see the three iHMP project sites for project-specific protocols:

Pregnancy and Preterm Birth
Onset of Inflammatory Bowel Disease (IBD)
Onset of Type 2 Diabetes
Member Organizations