Manual Pangenome - Githubissues

carpentries-incubator / pangenomics

Pangenome Analysis in Prokaryotes Lesson

https://carpentries-incubator.github.io/pangenomics/

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Manual Pangenome #40

Closed nselem closed 1 year ago

nselem commented 1 year ago

Develop episode 04-manual-pangenomes.md to explain the two-step process, you need a distance plus a clustering algorithm to calculate pangenomes. Chose a reduced-size example that runs in live-coding, some genomes, or some gene families making sure you exemplify core/shell and cloud genome. Faa files from annotations should be used. ❤️

HaydeePeruyero commented 1 year ago

Extraer familias para hacer un blast pequeño. Hacer las comparaciones de todos los genes contra todos los genes.

HaydeePeruyero commented 1 year ago

Families with bdbh algorithm

Czirion commented 1 year ago

The code is ready!

[x] Review the text of first two sections
[x] Review the text of third section
[x] Add an exercise

Major issue

[ ] Consider a similarity threshold in the BDBH algorithm