User: predeus
predeus • 480
- Reputation:
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- Russia
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- http://bioinf.me/research
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- APredeus
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- Joined:
- 5 years, 5 months ago
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about me
Posts by predeus
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... Hello all,
I am working on some bacterial genome assemblies that have been assembled using Pacbio reads only. I realized that I can make minor improvements to them (on the order of several SNPs and indels) by aligning Illumina data from the same strain to Pacbio assembly, and polishing it with Pil ...
written 6 weeks ago by
predeus • 480
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... SNPs and indels with annotations (silent/missense/nonsense, frameshift/in-frame), for example. ...
written 6 weeks ago by
predeus • 480
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... Maybe I did not make myself sufficiently clear. I have no problem choosing a classical genome browser (with one reference and one annotation) to view and analyze coverage, annotation, etc. Variant/coverage analysis for typical use cases (short reads aligned to a reference) are no problem as well.
...
written 6 weeks ago by
predeus • 480
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... Artemis Comparison Tool (ACT) is the tool related to Artemis, that does multi-genome visualization. It's very ancient and bad though, just painfully so.
Thank you for he anvi'o link, I will check it out though. ...
written 6 weeks ago by
predeus • 480
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... yes, of course. I think I should have specified that I was looking for a dynamic visualization - sort of like genome browser, but for 2 (or possibly more) genomes. ...
written 6 weeks ago by
predeus • 480
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... yes, I did mention it in the original post... it's very poorly maintained, it seems. And since it's a Java jar, if it fails, there's no real way to debug it - you just have to accept it. ...
written 6 weeks ago by
predeus • 480
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... Ah, thank you. This is very neat. ...
written 6 weeks ago by
predeus • 480
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... ha, that is a very creative use of minimap2 :)
at least there's a js visualization, worth a shot. Thank you. ...
written 6 weeks ago by
predeus • 480
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... Last update on the code is in 2011, publications are from 2000-2004. Is it really still relevant? Visualizations look pretty horrible too (by modern standards of course). ...
written 6 weeks ago by
predeus • 480
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9 follow
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... Hello all,
I was wondering if there are any modern tools for visualization of whole-genome alignment, with ability to add annotation, and maybe extract variants? I've tried Mauve and Harvest so far, but they seem pretty abandoned and work quite poorly.
Are there any modern projects you can recom ...
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