Minimap2 compatibility

[abayega]

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).

[weedcentipede]

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

Cheers.

[jason-weirather]

@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.

[abayega]

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.