Welcome to the project home for our NSURP research materials! The training website contains a much prettier (rendered) version of these materials - check it out!
This project is designed to facilitate learning bioinformatic techniques while working through a metagenomics project on publicly-available data.
During this project, you will learn how to:
- keep a detailed lab notebook
- interact with an HPC (we'll use Farm)
- install and manage software environments using conda
- download sequencing data and other files from the internet and public databases
- interpret and use different file formats in bioinformatics and computing
- conduct quality analysis and control for sequencing data
- determine the taxonomic composition of sequencing reads
- quickly compare large sequencing datasets
- build reproducible workflows using snakemake
- document workflows using git and GitHub
- troubleshoot errors during your analysis
The material in this repository was primarily written or aggregated by @bluegenes, @taylorreiter, and @hehouts. It adapts and builds on tutorials from the following sources:
- DIB-Lab Metagenomics Rotation Project: https://github.com/dib-lab/dib_rotation
- ANGUS: https://angus.readthedocs.io/en/2019/index.html
- HPC Carpentry: https://hpc-carpentry.github.io/
- Data Carpentry Genomics: https://datacarpentry.org/genomics-workshop/
- CICESE Metatranscriptomics: https://github.com/ngs-docs/2018-cicese-metatranscriptomics