Pangenome partitioning #29
Merged
Conversation
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
This introduces a greedy algorithm to partition pangenomes into more manageable chunks that will go into
seqwish/pggbfor "explicit" pangenome graph building. It builds on top of the latest fixes and changes inimpgto correctly query pangenome alignment (#23, #24, #27) and make transitive queries possible (#25, #26) and in a reasonable amount of time (#28). The algorithm is implemented as abashscript for simpler future exploration before re-implementing several steps to achieve better performance.This also adds an
Rscript to get a (still not super nice, but good enough) visualization of pangenome partitioning statistics that will help judge its quality. Here is an example on the yeast pangenome: