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iMAP: Integrated Microbiome Analysis Pipeline

NOTE: The new iMAP repo is being rebuilt to make it more reproducible. For more details, please refer to the Related Work section below.

⚠️ WARNING: Some sections (Parts) of iMAP are currently incomplete. We are diligently working on data exploration, focusing particularly on various visualization and statistical analysis techniques. Our team is committed to assisting users in uncovering insights and trends within the microbiome datasets and developing data-driven hypotheses to facilitate well-informed decisions and actionable insights. Users are encouraged to visit the site more frequently for updates.

IMAP-Repo Description GH-Pages
OVERVIEW IMAP project overview Link
PART 01 Software requirements for microbiome data analysis with Snakemake workflows Link
PART 02 Downloading and exploring microbiome sample metadata from SRA Database Link
PART 03 Downloading and filtering microbiome sequencing data from SRA database Link
PART 04 Quality control of microbiome next-generation sequencing reads Link
PART 05 Microbial profiling using MOTHUR and Snakemake workflows Link
PART 06 Microbial profiling using QIIME2 and Snakemake workflows Link
PART 07 Processing output from 16S-based microbiome bioinformatics pipelines Link
PART 08 Exploratory analysis of processed 16S-based microbiome data Link
PART 09 Statistical analysis of processed 16S-based microbiome data Link
PART 10 Machine learning analysis of processed 16S-based microbiome data Link


Citation

Please consider citing the iMAP article (see below) if you find any part of the IMAP practical user guides helpful in your microbiome data analysis.

Buza, T. M., Tonui, T., Stomeo, F., Tiambo, C., Katani, R., Schilling, M., … Kapur, V. (2019). iMAP: An integrated bioinformatics and visualization pipeline for microbiome data analysis. BMC Bioinformatics, 20. https://doi.org/10.1186/S12859-019-2965-4

Please, help to increase awareness of freely available microbiome data analysis tools. Current iMAP manuscript dimensions


Original iMAP!

Running Analysis within Docker Container (Default)

Running Analysis On Specific Platforms