Comments (2)
Aligning contigs from multiple supernova denovo assemblies to a reference assembly is a usecase I have as well.
Contigs can be megabases in size and I wish to have more global alignment behaviour so we can discover regions of high divergence between the supernova assemblies and the reference assembly.
We have large memory machines so could we crank up -w and -d to say 10,000 ?
Some discussion on appropriate settings for bwa mem would be highly appreciated.
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Use minimap2.
from bwa.
Related Issues (20)
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from bwa.