flashton2003

Mapping to repeats leads to deletions with low allele frequency

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Hello, I'm analysing some Cryptococcus neoformans (a haploid fungus) PacBio genome data. I noticed something strange when I was looking at some deletions which had low allele frequency. When only...

Perhaps it's just temporary, but https://yulab-smu.top/treedata-book/ seems to be down?

[feature] Update docs with details of how bactopia handles long read only data

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**Related To** - [ ] Bactopia **Is this related to a problem?** It's not well documented how bactopia handles long read only data. **Is this something you would like to...

Output mash tree or equivalent?

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Hi, It's nice that mob-suite tells me the plasmid in the reference database which is closest to each plasmid it identifies in my sample, but it would be good if...

Problem when running LMM tutorial

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Hello, We are running through the tutorial for the linear mixed model and are having some issues. We downloaded the data from [FigShare](https://figshare.com/articles/pyseer_tutorial/7588832), ran fsm-lite (can't see how to get...

Include nucleotide substitution for point mutations

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Hello, For organisms that have point mutation detection supported, amr-finder-plus reports the amino acid change (e.g. S83F for QRDR mutations for Salmonella). Would it be possible to also report the...

Issue with Lighter performance

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Hello, I'm not sure that Github issue is the best place for this, but it is the suggested channel for support so will give it a go. I had some...

problem with bactopia tools website

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I'm trying to access https://bactopia.github.io/bactopia-tools/ but it doesn't load, it just keeps appending latest to the URL, after a few seconds I end up with this https://bactopia.github.io/bactopia-tools/latest/latest/latest/latest/latest/latest/latest/latest/latest/latest/latest/latest/latest/latest/latest/latest/latest/latest/latest/latest/latest/latest/latest/latest/latest/latest/latest/latest/latest/latest/latest/latest/latest/latest/latest/latest/latest/latest/latest/latest/latest/latest/latest/latest/latest/latest/latest/latest/latest/latest/latest/latest/latest/latest/latest/latest/latest/latest/latest/latest/latest/latest/latest/latest/latest/latest/latest/latest/latest/latest/latest/latest/latest/latest/latest/latest/latest/latest/latest/latest/latest/latest/latest/latest/latest/latest/latest/latest/latest/latest/latest/latest/latest/latest/latest/latest/latest/latest/latest/latest/latest/latest/latest/latest/latest/latest/latest/latest/latest/latest/latest/latest/latest/latest/latest/latest/latest/latest/latest/latest/latest/latest/latest/latest/latest/latest/latest/latest/latest/latest/latest/latest/latest/latest/latest/latest/latest/latest/latest/latest/latest/latest/latest/latest/latest/latest/latest/latest/latest/latest/latest/latest/latest/latest/latest/latest/latest/latest/latest/latest/latest/latest/ and the page...

Hello, We've isolated some subsp salamaes for one of our projects. I have a few questions about the SISTR output for these isolates: sample | cgmlst_found_loci | cgmlst_matching_alleles | cgmlst_subspecies...

Hi guys, I'm trying to download the kraken2 gtdb database using google_download.sh. The output I get is ``` % Total % Received % Xferd Average Speed Time Time Time Current...