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there are three ways to do this.
* mapping based: map reads, call variants, build a variant call file (VCF), estimate ANI from VCF SNP calls.
* mapping based: create a new consensus genome based o…
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iHMP? or something else?
it'd be nice if it had a specific set of genome(s)... could do the hu et al one
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Hello,
If I wanted to do exact k-mer comparisons between genome assemblies could I simple use `sourmash sketch` with `scaled=1`?
Is this a stupid thing to do?
I have a limited set of bacterial…
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### Operating System
macOS
### Other Linux
_No response_
### Workflow Version
v1.2.0
### Workflow Execution
EPI2ME Desktop application
### EPI2ME Version
v5.1.14
### CLI command run
_No res…
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Hi Torsten,
Lots of bacterial genomes are lacking SRA data, preventing us from performing several reads-based analysis. I think you mentioned somewhere that "best reads are contigs", and do you rec…
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Hi, I'm using Jellyfish+Genomescope on pair-end NGS data. It seems like that Genomescope complains about failing to converge and the result seems not correct. I have tried changing kmer from 21 to 19,…
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I feel like this type of method would work as a fantastic competitor to bacterial whole genome alignment software such as Mauv/progressiveMauve. Have you tried validating this software with bacterial …
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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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Working with a database I created using bacterial, archaeal and fungal genomes, I am now getting the following trying to run it with some reads:
Error reading _ebwt[] array: 1352, 7627660928
…
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This issue contains monthly updates to an automatically ranked list of PubMed papers as candidates for curation in the Bioregistry. Papers may be relevant in at least three ways:
(1) as a new prefix…