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I used your script to convert nucmer delta file to bam file. I tried to open the bam file in Geneious, it said the bam format is not correct.
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## Problem description
Currently (version 0.2.0-beta2), `flye_end_repair.sh` is run after the assembly step to fix any potential issues with the region around the ends of circular contigs. At the end…
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Hello, I am trying to run analysis with mummer/nucmer 4 using a multithreaded approach.
I first ran nucmer/mummer3.23 via:
```
nucmer -maxmatch -l 100 -c 500 $ref $query -prefix out
```
Which w…
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_Originally posted by @sarah872 in https://github.com/widdowquinn/pyani/issues/20#issuecomment-440969428_
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Hi malonge,
Thanks for the useful tool. I have got three assemblies (one monoploid genome and two haplotype assemblies) of a diploid plant using HiFi+HiC. Because the haplotype assemblies had …
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Hi,
I am trying to install circlator on our HPC cluster. I am trying to use Singularity and convert the docker image, but I ran into an issue that I have been able to reproduce with the docker ima…
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Thank you for addressing my previous issue with nucmer detection ([#122](https://github.com/sanger-pathogens/circlator/issues/122)). However, having installed v1.5.5, I'm now having a different nucmer…
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Hi,
I get a error message when ran command as following:
nucdiff ../1D.fa ../chr1D_contig.fa . AK58VSCS
![image](https://user-images.githubusercontent.com/24313587/76403756-5a6a2d80-63c0-11ea-9d…
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Hi,
I am dealing with a large genome and therefore running quickmerge took a very long time, is there a way to run the quickmerge wrapper in multi-thread to accelerate the process? I check the wrap…
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Hi,
I am running Nucdiff on some data and I am getting the following error. I have run this exact script before on a different dataset which runs without any problem and I have doubled checked my f…