Emerging Technologies Librarian
Patricia F Anderson
Contact:
Taubman Health Sciences Library
1135 E. Catherine St.
Ann Arbor, MI 48109
1135 E. Catherine St.
Ann Arbor, MI 48109
615-1513
Website Skype Contact: rosefirerising
Human Microbiome Project
Methods, Protocols, Standards
National and international research standards, methodologies, and official protocols which impact on the professional practice of microbiomic research.
- Human Microbiome Project: Tools & Technologies"All software, online resources and standard operating protocols used in, or developed as part of the HMP, will be accessible here as they become available."
Microbiome Data Links
Databases which include data from microbiome research projects.
- Bioproject"A BioProject is a collection of biological data related to a single initiative, originating from a single organization or from a consortium. A BioProject record provides users a single place to find links to the diverse data types generated for that project."
- Biopsample"The BioSample database contains descriptions of biological source materials used in experimental assays."
Software Collections
Other sources to discover software tools used in microbiomics.
- Microbiome Utilities Portal (Broad Institute)Best one stop shop for microbiome software and utilities.
- BIOM Format"The BIOM file format (canonically pronounced biome) is designed to be a general-use format for representing biological sample by observation contingency tables. BIOM is a recognized standard for the Earth Microbiome Project and is a Genomics Standards Consortium supported project." Includes list of software based on this standard, including mothur, Qiime, and more.
mothur
mothur is an open source software package for the support of microbiome researchers data analysis needs, created by Patrick Schloss of the University of Michigan. "mothur is currently the most cited bioinformatics tool for analyzing 16S rRNA gene sequences. "
- MOTHUR"This project seeks to develop a single piece of open-source, expandable software to fill the bioinformatics needs of the microbial ecology community." Developed by Patrick Schloss of the University of Michigan.
- Introducing mothur: Open-Source, Platform-Independent, Community-Supported Software for Describing and Comparing Microbial Communities▿Original article introducing the MOTHUR software.
- MOTHUR on GitHubMOTHUR is open source, and this is where to find the code, just in case you want to tweak it.
- HMMCP - mothur Community Profiling"This dataset corresponds to over 5,700 samples and over 10,000 sequence preps. 16S variable region 3-5 (V35) was sequenced for the entire set of samples, and variable regions 1-3 (V13) and 6-9 (V69) for a subset of samples."
- MOTHUR WikiThis project seeks to develop a single piece of open-source, expandable software to fill the bioinformatics needs of the microbial ecology community. mothur is the most cited bioinformatics tool for analyzing 16S rRNA gene sequences and can be easily used to analyze data generated by Sanger, PacBio, IonTorrent, 454 and Illumina (HiSeq/MiSeq).
JCVI METAREP
METAREP is an software tool and dashboard used by many researchers for analysing genetic and genomic data. "JCVI Metagenomics Reports (METAREP) is an open source tool for high-performance comparative metagenomics. It helps scientists to view, query, browse and compare metagenomics annotation profiles from short reads or assemblies."
QIIME
- QIIME2 (Qualitative Insights into Microbial Ecology)"QIIME is an open-source bioinformatics pipeline for performing microbiome analysis from raw DNA sequencing data."
More Microbiome Software
- AmpliconNoise"AmpliconNoise is a collection of programs for the removal of noise from 454 sequenced PCR amplicons. It involves two steps the removal of noise from the sequencing itself and the removal of PCR point errors. This project also includes the Perseus algorithm for chimera removal."
- Explicet"Explicet is a free to use, open source software package (GPLv3) available for Windows, Mac, and Linux that facilitates the exploration and visualization of taxonomy-based microbiome datasets (a.k.a. OTU tables)."
- LOTUS (Less OTUs)"LotuS is aimed at scientists and bioinformatician that want a simple pipeline that is streamlined to a core functionality of creating OTU and taxa abundance tables, at very fast speeds (e.g. processing an 8GB 16S miSeq run takes ~ 30 min on a laptop). LotuS does not include numerical analysis of samples, instead we designed LotuS output to be easily integrateable into existing workflows in e.g. statistical programming languages like R, QIIME/mothur or Matlab."
- mockrobiota"A public resource for microbiome bioinformatics benchmarking using artificially constructed (i.e., mock) communities."
- NGS Preprocessor"Usually it takes several steps to remove or filter contaminants from RNA-seq sequences to make them suitable for alignment and analysis. This requires users to type several commands and specifies parameters for different commands for each sequence file." Includes gist, genepuddle, and gargle.
- otupipe"Otupipe was a bash script for OTU clustering based on USEARCH. This page is retained for historical interest because a script based on otupipe was used to create the published QIIME results for the Human Microbiome Project (HMP)."
- Qiita"Qiita (canonically pronounced cheetah) is an entirely open-source microbiome storage and analysis resource that can run on everything from your laptop to a supercomputer. It is built on top of the widely used QIIME package, and enables the exploration of -omics data."
- UPARSE"UPARSE generates OTUs that are far superior to state-of-the-art methods including QIIME, mothur and AmpliconNoise on mock community tests. OTU representative sequences are more accurate predictions of biological sequences, and the number of OTUs is much close to the number of species."
Last Updated: Jan 16, 2024 10:59 AM