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rki-mf1 / covsonar

A database-driven system for handling genomic sequences of SARS-CoV-2 and screening genomic profiles.
GNU General Public License v3.0
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minimap2 as alternative alignment tool #10

Closed silenus092 closed 1 year ago

silenus092 commented 3 years ago

In GitLab by @hoelzer on May 27, 2021, 09:54

Could be interesting to test minimap2 as aligner instead of EMBOSS-stretcher

E.g. the developer just announced that

Minimap2 v2.19 released with better and more contiguous alignment over long INDELs and in highly repetitive regions, improvements backported from unimap. These represent the most significant algorithmic change since v2.1. Use with caution.

https://twitter.com/lh3lh3/status/1397736460174888961?s=19

I would be interested in how well minimap2 is able to accurately align genomes over long N stretches.

silenus092 commented 3 years ago

In GitLab by @s.fuchs on May 30, 2021, 20:08

indeed, thx! I'll test it!

silenus092 commented 3 years ago

In GitLab by @s.fuchs on Aug 24, 2021, 08:22

Good idea, I am working on it!

stephan-fuchs commented 1 year ago

Minimap2 was excluded from our selection of tools as it does not provide global alignment. However, in CovSonar2 (https://github.com/rki-mf1/covsonar/tree/dev/covsonar2-alpha), we use semi-global alignment provided by PARASAIL which produces optimal results.