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HSPH Microbiome Analysis Core

Directors: Huttenhower, Curtis, Ph.D.; Wilkinson, Jeremy E., Ph.D.

Location: Biostatistics Department, Bldg SPH1, 4th Floor, Room 412A, Harvard School of Public Health, 655 Huntington Ave, Boston, MA 02115


The HSPH Microbiome Analysis Core (HMAC) provides analyses of microbial amplicon (16S rDNA and ITS), metagenomic, metatranscriptomic, and metaproteomic sequence data. The HMAC offers support at all stages of research, from study design through proposal drafting to data analysis and interpretation. Core activities include consultation, provision of services, and fully collaborative grant-funded investigations.

The HMAC has extensive experience with large cohort-based multi’omic data collections, from bioinformatics processing to systems biology and integrative data analysis. We also carry out analysis of individual microbial genomes, and maintain a richly annotated catalog of all currently available microbial genomes as well as a large database of cross-species microbial functional data.






  • Data analysis and interpretation ( Data analysis service )

    - Quality control (QC) processing of raw sequence data using the KNEAD bioinformatics workflow, an implementation of open-source sequence filtering algorithms.
    - Meta-omic data analysis using Huttenhower Lab Tools (https://bitbucket.org/biobakery/biobakery/wiki/Home).
    - Amplicon (16S rDNA and ITS) data QC and analysis: QIIME, mothur, UPARSE, RDP Classifier.
    - Multivariate analysis, network analysis and integration of high-dimensional microbial data using publicly available statistical libraries (e.g. MaAsLin, Vegan, phyloseq, mixOmics, NeAT, etc.)
    - Custom implementation of algorithms for analysis of microbial datasets.

  • Data handling ( Support service )

    For computing infrastructure, the Core is using Odyssey, the FAS Research Computing cluster. Your meta’omic data is housed on dedicated and regularly backed-up network storage drives.

  • Free consultation on study design and data analysis ( Support service )

  • Grant proposal review, drafting, and power analysis ( Support service )

  • Manuscript: review, drafting response to reviewers ( Support service )

  • Wet lab services – small-scale ( Material analysis service )

    - Extraction of microbial RNA/DNA from host and environmental samples.
    - Sequencing of metagenomic, metatranscriptomic, and amplicon libraries.

    Service models: fee-for-service ($150/h), grant percent effort.


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Last updated: 2019-02-11T09:19:37.249-06:00

Copyright © 2016 by the President and Fellows of Harvard College
The eagle-i Consortium is supported by NIH Grant #5U24RR029825-02 / Copyright 2016