readme_local_wishlist.md

Wishlist for local analysis upgrades

Modules with additional functionality

In the future, we should add the following modules to the local analysis script:

• Adaptive evolution analysis: look for parallel evolution and compute dN/dS (N/S compared to neutral model)
  • Status: Arolyn has a nice version in Matlab, but it hasn't been coded in python yet.
• Gain/loss analysis: use coverage matrices to find genes that are missing from some samples in the lineage
  • Status: Arolyn and Felix developed an amplification/deletion python script which could be incorporated into this version. Arolyn also made a gain/loss script in matlab which could be re-coded in python.
• Additional treemaking: implement treecounting script
  • Status: This was implemented in previous python analysis script (should be relatively easy to incorporate).

Changes to existing functions

• Rewrite functions that generate genome annotations from scratch (they are messy)

Environment/python version

• Upgrade to Python 3.11 (for faster CPython)

Table of contents

Main Lieberman Lab pipeline README

• Snakemake pipeline
  • How to run the snakemake pipeline
  • Technical details about the snakemake pipeline
  • Wishlist for snakemake pipeline upgrades
  • Helpful hints for using the command line
• Local analysis
  • How to run the local analysis script
  • Wishlist for local analysis upgrades
  • Python best practices