Github

GitHub: https://github.com

Track and manage changes to your code & files

Store and label changes at every step

Small or large projects

Collaborate on projects and minimize conflicting edits

Works on multiple platforms (MacOS, Windows, Linux)

Website for github, cutadapt repository

Conda/Mamba environments

• Isolated spaces for each project with specific tool versions

• Manage Python versions and dependencies

• Install packages and software directly into environment

• Stable and reproducible place to run code and applications

• Not limited to Python, can run bash, Rscript

• YAML configuration file to create or export and transfer an environment

• Public repositories for sequence data - required for most journals

  • NCBI: https://www.ncbi.nlm.nih.gov
  • Ensembl: https://www.ensembl.org/index.html
  • Always document and archive changes, especially if unpublished:
  • • genome assembly versions
  • • sequence data: SNPs, isoforms

Websites: NCBI, Ensembl, Santa Cruz