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Published 20 hours ago • verified publisher icon jason-weirather

Minimap2 compatibility

Open abayega opened this issue 6 years ago • 3 comments

Hi,

although it clearly says that you have tested AlignQC with GMAP, I wonder if you have also tested Minimap2 and can recommend using Minimap2. Minimap2 runs very fast and Minimap (not exactly Minimap2) has recently been shown to be the most sensitive to Nanopore (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5408847/, the application here was DNA overlaps).

abayega avatar Apr 26 '18 02:04 abayega

Hi, Actually I've only used this program with Minimap2, and it worked absolutely wonderfull.

Cheers.

weedcentipede avatar May 09 '18 23:05 weedcentipede

@OnlyHigh Hi Luis thanks for the report. I'll update our documentation to reflect it. We are preparing a manuscript for the tool and I'll look into running minimap2 on the dataset so I can make mention in the paper too. Thanks! I'll leave this open till I can get the docs updated and the test run.

jason-weirather avatar May 09 '18 23:05 jason-weirather

Thank you, I have been running with Minimap2 -x splice and AlignQC has probably only complained once when it could not load the sequences but otherwise it runs beautifully on Minimap2 output. I just want to be sure there's nothing unsupported hidden in the Minimap2 ouptut.

abayega avatar May 10 '18 00:05 abayega