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Dear Friends,
I don't have reads, but assemblies (one or mere contigs) of S. pneumoniae.
How can I assign the serotype?
seroBa doesn't look like to support fasta input right?
Bests,
Alex
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- [ ] Literature review on Vibrio Pathogenicity Islands- Vanessa, Brian and Latifah.
- [ ] Work out the relationship between VPI and CTX phage- Vanessa, Brian and Latifah.
- [x] Get 10 cholera seque…
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Input of definitions and list of values can be found:
https://github.com/pha4ge/Wastewater_Contextual_Data_Specification/tree/main/Template
The following table combines the info from above and add…
edsu7 updated
3 months ago
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Hi..any suggestions on how this error was resolved for you? I am using singularity image on centos7 without admin previleges.
_Originally posted by @sreerampeela in https://github.com/sanger-pathog…
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Dear seroba team,
I have run into an issue where serotyping won't run unless I explicitly set coverage.
```
root@d2d570a8775d:/# seroba runSerotyping seroba/database/ data/testsample_1.fastq.gz…
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Hey everyone,
I am getting a KeyError when I am running seroba on my test data.
```
Traceback (most recent call last):
File "/home/user/.local/bin/seroba", line 86, in
args.func(args)…
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Dear seqSerotyper team,
I recently download seqSerotyper and Run the script as suggested:
`Rscript seqSerotyper.R -dataFile /data/spneu/data_file.txt -srcDir /home/user/seqSerotyper/bin`
Howeve…
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Hi, i am trying to run PAst for pseudomonas serotyping and i encountered following error-
****./PAst.pl /home/bvs/neelam/ncbi-blast/bin /home/bvs/neelam/out /home/bvs/neelam/genome/fna /home/bvs/n…
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I have minimap2 and mash in my environment, so I thought I could install kleborate with pip (`pip install kleborate`). To me, it was kind of like https://kleborate.readthedocs.io/en/latest/Installatio…
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Hi Folks,
I have recently installed PneumoCaT onto our Galaxy instance (which is connected to our HPC cluster using PBS).
Unfortunately, when I try to run it, these are the ouputs I am getting i…