User: predeus

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predeus480
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Russia
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http://bioinf.me/research
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APredeus
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5 years, 5 months ago
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Posts by predeus

<prev • 77 results • page 1 of 8 • next >
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Huge jump in plasmid coverage - any idea why?
... 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 ...
pilon illumina bacteria pacbio written 6 weeks ago by predeus480
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Comment: C: Modern software for whole genome alignment visualization
... SNPs and indels with annotations (silent/missense/nonsense, frameshift/in-frame), for example. ...
written 6 weeks ago by predeus480
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Comment: C: Modern software for whole genome alignment visualization
... 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 predeus480
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Comment: C: Modern software for whole genome alignment visualization
... 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 predeus480
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Comment: C: Modern software for whole genome alignment visualization
... 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 predeus480
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Comment: C: Modern software for whole genome alignment visualization
... 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 predeus480
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Comment: C: Modern software for whole genome alignment visualization
... Ah, thank you. This is very neat. ...
written 6 weeks ago by predeus480
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Comment: C: Modern software for whole genome alignment visualization
... 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 predeus480
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Comment: C: Modern software for whole genome alignment visualization
... 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 predeus480
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Modern software for whole genome alignment visualization
... 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 ...
whole-genome alignment harvest visualization mauve written 6 weeks ago by predeus480 • updated 6 weeks ago by h.mon13k

Latest awards to predeus

Popular Question 11 weeks ago, created a question with more than 1,000 views. For Get a complete GSM-to-SRX/SRR table
Prophet 3 months ago, created a post with more than 20 followers. For Duplicates on Illumina
Popular Question 11 months ago, created a question with more than 1,000 views. For Chip-Seq Of Conventional Tfs: What Are The Peaks W/O The Motif?
Commentator 12 months ago, created a comment with at least 3 up-votes. For C: How To Convert Gencode Gtf Into Bed Format ?
Supporter 13 months ago, voted at least 25 times.
Popular Question 15 months ago, created a question with more than 1,000 views. For How To Determine If Library Is Strand-Specific
Appreciated 15 months ago, created a post with more than 5 votes. For Duplicates on Illumina
Good Question 15 months ago, asked a question that was upvoted at least 5 times. For Duplicates on Illumina
Student 15 months ago, asked a question with at least 3 up-votes. For Duplicates on Illumina
Popular Question 23 months ago, created a question with more than 1,000 views. For Chip-Seq Of Conventional Tfs: What Are The Peaks W/O The Motif?
Popular Question 2.4 years ago, created a question with more than 1,000 views. For Find All Annotated Rrna (Rdna) Sequences
Popular Question 3.6 years ago, created a question with more than 1,000 views. For How To Determine If Library Is Strand-Specific
Popular Question 3.6 years ago, created a question with more than 1,000 views. For Find All Annotated Rrna (Rdna) Sequences
Teacher 3.9 years ago, created an answer with at least 3 up-votes. For A: Too late to switch to Bioinformatics?

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