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hillerlab / make_lastz_chains

Portable solution to generate genome alignment chains using lastz
MIT License
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Full scale run creates too many lastz jobs #28

Closed kirilenkobm closed 1 year ago

kirilenkobm commented 1 year ago

If the reference has many short chromosomes/scaffolds, it results in a tremendous amount of last jobs (hundreds of thousands). The partitioning step must handle such cases. For example, by merging such chromosomes/scaffolds into "buckets", processed as a single unit by run_lastz.py

kirilenkobm commented 1 year ago

Created branch https://github.com/hillerlab/make_lastz_chains/tree/fixed_partitioning where this issue is going to be fixed.