• Version control

• Environment management

• Data storage

• Containers

• Tool/software maintenance

Version Control

GitHub

Click the following link to visit the GitHub site: 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

Envoronment Management

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

Storing Results

Public repositories for sequence data - required for most journals

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• Always document and archive changes, especially if unpublished: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

Containers

• Containers are portable environments that run across different computing environments
• They contain packages, software and dependencies that remain isolated from host infrastructure
• Standalone unit of software and can produce same results on different machine or server