MetaSUB Bioinformatics¶
MetaSUB is a global consortium studying the microbiome of the urban environment. Cities are complex environments where organisms must adapt to natural challenges, human activity, and substances which would rarely be encountered in nature. Despite these challenges rich ecosystems exist in cities including complex microbiomes. MetaSUB’s goal is to understand what impact these microbes have on human health by building a global molecular map of our cities.
This site covers the practical issues of working with MetaSUB data. This site includes information on: - How MetaSUB data is stored - How MetaSUB data is versioned - What Programs are used to analyze data - How to contribute to MetaSUB’s projects
Programs and Resources¶
We use a number of programs for bioinformatics at MetaSUB. Everyone in MetaSUB is welcome to contribute to any relevant codebase including filing issues.
Public Resources¶
Metadata for Sequenced Samples, A fully reproducible metadata table for all sequenced samples.
The Core Analysis Pipeline, A pipeline for analysis of short read metagenomic data.
The Core QC Pipeline, A pipeline to perform quality control of samples.
Data Table Generator, A tool to build data tables from the output of the CAP
Private Resources¶
Figure Generators, code to generate figures and tables for publication and exploration. Available as a private GitHub repo
MetaSUB Data Packet, raw data tables from running the CAP on MetaSUB samples. Available on Dropbox and as a private GitHub repo.
Public Utilities¶
Bioinformatics Management, Policies, and Communications
Utility Scripts, Used for managing metasub data, transferring storage, and handling analysis. Serves as a catch all for small programs.