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rrwick / Trycycler

A tool for generating consensus long-read assemblies for bacterial genomes
GNU General Public License v3.0
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trycycler reconcile: multiprocess get_pairwise_alignments #63

Closed danpal96 closed 1 year ago

danpal96 commented 1 year ago

trycycler v0.5.4

One of the slower steps in trycycler reconcile is the call of the get_pairwise_alignments function https://github.com/rrwick/Trycycler/blob/c00d56f2547de4170a425cf610a6d3f2eeec5830/trycycler/pairwise.py#L20

I think the for loop could be parallelized and if you want I can make a PR. Regards, Daniel Palma

rrwick commented 1 year ago

You're right - that step can be a bottleneck, especially for longer contigs.

You're welcome to put together a PR, if you'd like - thanks!

rrwick commented 1 year ago

Thanks for the PR 😄