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We discussed this briefly in person on Monday 14 October, but to put this in writing:
The details differ but most if not all of the ANI methods have some threshold below which they find no meaningf…
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As mentioned in rotary-genomics/rotary-utils#8, the [`merge` module from circlator](https://github.com/sanger-pathogens/circlator) (a very helpful package!) is currently used to guide the final step i…
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Dear gmarcais,
I have downloaded mummer-3.9.4alpha.tar.gz by wget, untar and installed it as instructions. It looks fine. But when I ran dnadiff (with or without full path) some errors were appeared …
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Hi aganezov,
First of all thank you for this promising program.
I processed some assemblies and scaffolds with fasta2camsa to create points files.
But these are running in single thread and i…
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ERROR: mummer and/or mgaps returned non-zero
ERROR: Could not parse delta file, nucmer.delta
Hi, I am getting this error while running ABACAS with the following params.
$ perl abacas.1.3.1.pl -b -N…
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@martinghunt Could you please clarify two points:
(1) Does pymummer support [mummer4](https://mummer4.github.io/)?
(2) Does it support promer in addition to nucmer?
Thanks!
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Hi,
The program seems to fail with the example datasets provided in the repo. I did a conda installation with the yaml file running on MacOS
Please help troubleshoot it.
`$mummer2circos -l -r …
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Users often have a reference genome and a set of contigs. Add the option to do a nucmer mapping to the reference genome in order to order/orient the contigs into a pseudo molecule before running.
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We want to include `sourmash` as an alternative for calculating ANI values. This will be a new feature, currently not available in the existing `pyANI`, so we need to investigate the best approach in …
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When I run circlator ```circlator test_output```, I get error messages at the merge step. It seems to be a problem with running nucmer:
```Running Circlator on test data...
Made output directory.…