Markus Schmidt comments

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                                            Markus Schmidt

Does SAMBA list changes that were made to the assembly somewhere?

No, from the output files I could not figure it out. However, I am running SAMBA in the mode, where it is only allowed to fill in gaps. So i...

Human genome

Hi, This repo is for two seperate tools: - MA, the aligner. MA works for the human genome. - MSV, the structural variant caller. MSV only works with small genomes...

redirect sam to standard output for piping

Hi, `-o /dev/stdout` should do it! Sincerely, Markus

redirect sam to standard output for piping

Hi, as far as i know each process should have it's own /dev/stdout. https://unix.stackexchange.com/questions/574597/how-dev-stdout-is-pointing-to-different-process-separately-in-linux Markus

closely related species as a reference for seed

Hi, Generally speaking, it is possible to align against any genome you want. The less related the genome, the more the aligner will struggle to produce good alignments. By adjusting...

Preset for PacBio CCS?

Hello, Currently, we do not have a special setting for HiFi PacBio. Please use the PacBio presetting as fallback until we have fixed this issue. However, special settings for HiFi...

MinKNOW run report read length estimates are way off for longer reads

I think the same thing is happening to us. You saved me a lot of work figuring out where these discrepancies come from. Thanks for looking at this in so...