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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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Dear Lennard,
is the tool seroba still maintained?
We had issues with the installation via conda and mamba.
#Standard installation from readme.md
`conda install -c bioconda seroba`
--> error …
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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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Dear MUMmer develop team,
I am trying to use NUCmer together with mummer plot to compare different assemblies of the same plant genome (~500Mb) with a finished genome of a relative species and my …
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Currently, if `f_ident` is < 10%, the user receives a warning: `too few identifiable hashes; f_ident < 10%. provide a lineage for this genome.` Given that this parameter was selected randomly, we may …
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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.…
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I have tried running installation with python3.6, 3.7, and 3.8 and I get a similar error message with each:
```
$ python3.6 -m pip install pymummer
Collecting pymummer
Cache entry deserializatio…
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When users want to included genomes for which they do not have access to fastq files - the current pipeline runs nucmer (pair-wise alignment) and calls SNPs using mummer. Ideally, reads should be simu…
nknox updated
9 years ago
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Hi,
I am aligning two Drosophila assemblies using nucmer -maxmatch (nucmer --maxmatch -t 128 -g 1000 --prefix foo asm1.fasta asm2.fasta). I got the following error -
`ERROR: failed to merge alignm…
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Hi, Alonge
Can `RagTag` add `wfmash` as alinger? It also ouput the paf file and is much faster than minimap2 or nucmer on high repitive plant assemblies.
baozg updated
2 years ago