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Hello,
I used digIS on a large number of bacterial genomes, and while IS belonging to the IS3, IS4, IS5, IS200/605 and ISNCY are reported in the .csv and in the .gff file, they're not listed as be…
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Hi Matt,
A girl in my lab is trying to set up ITEP with some bacterial genomes. She ran into an issue: convertGenbank2table.py fails because some of here genbank files (downloaded from RAST) have join…
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Hello everyone,
I building GTDB databases to be used along with Kraken2. I was wondering if it was possible to add viral refseq sequences while building kraken2 databases? GTDB consists of archaeal a…
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Hi,
I have a set of paired-end reads from bacterial RNA. Since the reference genome I'm using has a gene that's overlapping between the beginning and the end of the chromosome, I was wondering how ST…
EBosi updated
3 years ago
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In https://github.com/ekg/freebayes/issues/419 @tseemann [asked if vg was ready for bacterial pangenomics](https://github.com/ekg/freebayes/issues/419#issuecomment-377646948). My response better fits …
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Note also Ben's lunchtime verbal comment of cutting down magicblast-against-"bacteria" [or other large db] to look only at representative bacterial genomes (instead of all) as a coarse-grained option.…
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I tried predicting the genomic islands of bacterial genomes but somehow all the start and end positions of the treasureisland are rounded up. something like this:
![image](https://github.com/pr…
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**Project:**
I would like to make an open-source, readily available automated pipeline to close bacterial genomes with long read technologies and then fixing errors by mapping short reads to them. Fo…
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Hi,
I'm using a lot panaroo for a research project. I generated a gene_presence_absence matrix from 1500 bacterial genomes.
Then I used this matrix to train a supervised machine learning model. I go…
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Hi,
I run olivar on Bordetella pertussis genome. However, The progress bar remains at 0% without any changes.
![image](https://github.com/user-attachments/assets/394289ad-b24a-4a8e-8dcb-0f39c60e942…