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  1. N

    Reporting of alignments

    Wow that would be great.
  2. N

    Reporting of alignments

    Hi Benjamin, we would definitely need a cutoff of some kind so that only alignmentsthat actually make sense are reported. At the moment we use quite a stringent e-value cutoff for that and then use the top argument in the LCA step. That way you can change that parameter without redoing the...
  3. N

    Reporting of alignments

    Hi Benjamin, we've been playing around with the parameters that can be used to limit the reported alignments. We can't write all alignments to file due to hard drive limitations. So at the moment we are using thek or the top parameter. However, we do run into problems when we have species with...
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    Only load the reference once when mapping several samples

    Hi Benjamin, thanks for the fast reply. We would appreciate any reduction in computational time in the future. Cheers, Nicole
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    Only load the reference once when mapping several samples

    Hi, I have to map about 100 samples against nr. As far as I can tell, Diamond uses a significant amount of time (20-30 min?) to load the reference for every sample. Would it be possible to implement something like a shared reference (e.g. STAR loads the reference only once until it is...
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