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serotypefinder is a tool to mimic traditional serotyping in E. coli
The tool is a bit broken in the current state on bitbucket, so needs the following in order to use the committed settings. We could…
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Similar to what is required for Ecoli serotyping, capsule typing (**k typing**) should be added for _Klebsiella pneumonia_. We need to look into what tools are used to do this. Perhaps it’s the same a…
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Hi @kbessonov1984,
Thanks for the great tool!
I noticed that there appears to be a mismatch between ECTyper defaults, help message descriptions and the ECTyper manuscript.
Specifically these …
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**Description**
Bactopia running LisSero on Enterococci.
Ultimately ends run with:
```
Command exit status:
1
```
due to
```
[c.medib@cl1(hawk) 7d09be3242d017b01475b293b27091]$ cat .comma…
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On a sample, SeroBA encounters a fatal Python error
```
cluster detected 1 threads available to it
cluster reported completion
cluster_3 detected 1 threads available to it
cluster_3 reported co…
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Hello Harry, while executing the `gps-unified-pipeline` on a batch of 12 samples (FASTQ sequences), I encountered following error on one of my sample:
```
ERROR ~ Error executing process > 'PIPEL…
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see also bactopia
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I want to link your workflow to other workflows.
Could you 'emit' the fastq files and contig files in [main.nf](https://github.com/CDCgov/phoenix/blob/main/main.nf)? (And any additional files that…
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What reference should one use if there are multiple serotypes of a Virus. I understand that sequences belonging to each serotypes must be aligned separately but what if there is no RefSeq available fo…
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