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I'm trying to run PHIST on a single viral contig vs a large database of gzipped bacterial genomes. The program finishes without errors, but stops after the first ~715 reference genomes and reports the…
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Hi!
I have a big problem with last mash version (2.2).
When I want to calculate distance matrix between 2 genomes, it returns a binary matrix (p-value is either 0 or 1).
I tried with a fake geno…
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I know that some people have/are using Taxonium for bacterial genomes. I suspect that this probably poses some issues with e.g. the number of mutations on each branch which might get overwhelming. If …
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the low complexity filter has a fixed default 30%
that is priobably ok for genomes with 50% GC
but if my bacterial genome say has 78% GC, then statistically 30% might throw away too much
might be c…
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Hi Ryan,
I am using Trycycler to assembly 90 bacterial genomes from fish guts. It is an amazing and very helpful tool. I was able to obtain circular, > 98 % completeness, and very good coverage in al…
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## chord diagram
- [x] chordDiagram: Color gradients between groups #313
- [ ] In circos.heatmap, support border.color as a vector #308
- [ ] calc_gap() when it is not a two-group chord diagram …
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I just had my phylophlan run crash after 5 days and would appreciate any help.
I'm running version 3.0.2 installed via conda. I am trying to run phylophlan on a collection of bacterial isolate geno…
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Hi @gbouras13 ,
I use hybracter to assemble bacterial genomes and plasmids from long read sequencing. I want to assemble single plasmids from long read sequencing but hybracter does not work with o…
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Hi,
I have just installed homopolish and was trying to run it on assemblies of a set of _Polaromonas_ isolates, but I keep getting the 'less than 5 closely-related genomes' error message and I don't…
Dwrgi updated
2 years ago
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it doesn't look like complete protein fasta
I have blastp random sequence ">1119" from it - no hits into nr.
I have blastp first 80 sequences - only very weak hits.
"In this step, we run all pr…