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HI,
I used vRhyme with the default settings on my assembled contigs. I concatenated contigs from the same bins into a single fasta file using the provided bin sequences.py script.Later, I used …
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Hi Mike,
Recently, I ran cenote-taker2 and blastn against nt database & diamond against nr database with the contigs assembled by Megahit. I found that about 10000 sequences were classified as viruse…
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Hi,
My assembled contigs have headers as
>c_000003956504
>c_000004841845
>c_000004821562
which matches with the VAMB bin headers. But when I run PHAMB, I get bin headers as :
>1470111
>…
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Thanks for the very nice tool! I had run this tool on viral contigs. No error for the microdiversity part but show below error message for macrodiversity part. Could you provide some guidance on how t…
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I need to count the reads mapped to my viruses found via VirSorter2. However, I've already mapped to the contigs and I would like to use featureCounts to pull out the reads mapped to the viruses (not…
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Hi,
I compared the results that I obtained using vibrant contigs before and after running phamb using checkv
Before
|checkv_quality |n| mean |sum |max|
|---|---|---|---|---|
|Complete |557 |46…
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I'm running metaviral SPAdes with low-complexity (2-5 viruses) samples, and while it successfully works with most of them, three of them are consistently failing without warnings. The logfile reports …
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I have recently used VIBRANT with a metagenomics dataset with very good results, and I wonder if VIBRANT can also be run skipping the recovery step. I have few hundreds viruses that I recovered from s…
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Hello,
I was wondering how exactly VirSorter defines a prophage regions and if there is a way to get the coordinates of the prophage regions identified?
Thanks,
Niamh
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#### what is multiPhATE
[multiPhate](https://github.com/carolzhou/multiPhATE)
* fully automated computational pipeline for identifying and annotating phage genes in genome sequence
* controled by a…