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uio-cels / NucDiff

In-depth characterization and annotation of differences between two sets of DNA sequences
Mozilla Public License 2.0
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why --maxmatch is hard code #9

Closed slbai01 closed 4 years ago

slbai01 commented 4 years ago

Hi,

Thanks for your work.

I don't understand why the --maxmatch parameter is hard code when doing nucmer. Does this significantly affect the variation calling results?

I need to make a comparison of two larger genomes, even if I use mummer4 for chromosome comparison, if I add --maxmatch parameter, it is still very slow, each pair of chromosomes may take half a month, and the filtering result file will take a long time, this is unacceptable to me, so I want to use the --mum parameter.

Thanks

Shenglong

kseniakh commented 4 years ago

Hi,

--maxmatch is hard coded since this is the best option for detection of repeat-related differences. However, you can always run mummer yourself with any input parameters you like and use mummer output as input for nucdiff.

Ksenia