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lh3 / minigraph

Sequence-to-graph mapper and graph generator
https://lh3.github.io/minigraph
MIT License
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Evaluate the Performance of sequence-to-graph mapping in minigraph and GraphAligner. #60

Closed gsc74 closed 2 years ago

gsc74 commented 2 years ago

I want to evaluate the Performance of sequence-to-graph mapping as shown in Table 2 in minigraph, for both minigraph and GraphAligner, I'm able to get numbers for minigraph with using paftools.js mapeval minigraph_output.gaf. [paftools.js] Output: Q 60 2778043 13768 0.004956007 2778043 Q 59 828 7 0.004957049 2778871 Q 58 794 6 0.004957792 2779665 Q 57 754 6 0.004958605 2780419 Q 56 838 5 0.004958909 2781257 Q 55 756 4 0.004958999 2782013 ........ ........ While using same command paftools.js mapeval GraphAligner_output.gaf Output : Q 60 2907330 2907330 1.000000000 2907330 Q 58 1 1 1.000000000 2907331 Q 56 18 18 1.000000000 2907349 ............ ............. @lh3 , I want to know what is the difference between gaf output of minigraph and GraphAligner, and why paftools.js is giving right numbers for minigraph while wrong numbers for GraphAligner.

lh3 commented 2 years ago

You need to convert to the stable coordinate with misc/mgutils.js stableGaf

lh3 commented 2 years ago

FYI: the master branch has just been updated with more accurate alignment.

cjain7 commented 2 years ago

FYI: the master branch has just been updated with more accurate alignment.

This is good news. Can we expect a stable release of minigraph in near future? Also, there were pre-built graphs provided in minigraph manuscript. Can we expect new human rGFA graphs now?

lh3 commented 2 years ago

Can we expect a stable release of minigraph in near future?

I hope to release the current github HEAD in this week. After the release, I will try to improve the performance of minigraph for species of higher diversity (see #62). In this case, full WFA is too slow. I need to implement heuristics in miniwfa and see how heuristics affect graphs.

Can we expect new human rGFA graphs now?

For now, the most comprehensive human graph is the one I built for HPRC with v0.14. Here is the zenodo link. I will update the zenodo repo with graphs generated with the current github HEAD.

cjain7 commented 2 years ago

Thank you!