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If a significant change in methylation is detected, at which base pair is this change? Is it the position indicated by the pos column or perhaps the middle of the 5-bp kmer?
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**Versions**
poppunk 2.6.0
pp-sketchlib 2.1.0
**Command used and output returned**
Running poppunk in a conda environment in WSL2-Ubuntu
1206 genomes from one bacterial species (had already…
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Hi Oskar
I am facing an issue with running binny at PBS like server.
After it finishes 8/8 jobs, it's complaining about establishing connestion to network:
"Failed to establish a new connectio…
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## Expected Behavior
Cluster Uniref90 after it has been translated into a 5-letter alphabet. Cluster it to 90% identity and 80% overlap (similar to how Uniref90 was initially generated).
## Current …
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Hello,
I ran wenganM using ~60X Illumina coverage and ~10X Nanopore coverage (I know higher depth than this is best but it is what I have), for an expected 2Gb mollusc genome. Wengan finished in
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Dear Camille,
Many thanks for making the "Sketching in sequence bioinformatics: methods and applications" slides open source. Several questions related to bottom-s MinHash, One Permutation MinHash …
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Hi, I'm new to using SPAdes so I don't know how to enter some commands
Could someone tell me how to add the pipeline commands, I already ran my sequence, it stayed in k55 and it sends this error mess…
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Hello,
When I used Kmer=21, the genomescope graph is as follows:
When I used Kmer=27, the…
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Hello！Thank you for the tools you developed. When I use a custom database to identify strains, it give these error:
`terminate called after throwing an instance of 'std::runtime_error'
what(): Un…
wsyjh updated
7 months ago
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```
Some stats programs have things like kmer (with -K) reports and probe-id
counting (with -D).
These programs can consume a lot of RAM (>10GB), even with the highly efficient
sparsehash library o…