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Hi Simon,
I am trying to identify viral auxiliary metabolic genes (AMGs) using VirSorter v2.2.4 and DRAM v1.2.0 (viral mode; --skip_trnascan). The “viral-affi-contigs-for-dramv.tab” file has been…
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Hi Kris (and Karthik),
My student is trying to bin contigs identified by VirSorter using vRhyme. He is using as input contigs identified by VirSorter as viral, as well as sorted bam files that were…
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Hello
I have two viral contigs of approximately 3500bp from the same region of a genome. The two contigs differ by just 1%. Virsorter is run as:
virsorter run -w test.out -i test.fa --min-length 150…
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Hi,
I have used VirSorter2 to identify the viral genomes from the metagenome assemblies successfully. The command I have used was "virsorter run --prep-for-dramv -w DRTY10_201912_sfd_ge10kbp.out_v2 -…
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Hi, thanks for your very useful tool, and the one I am using it version 1.9.0. I have extracted viral contigs from metagenomic sequencing data of stool, and now want to estimate the relative abundance…
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Hi thanks for the great tool.
I am trying to calculate ANI between multi-contigs bins, where each viral bin consists of multiple contigs.
However, length estimate is different from the original one,…
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Hi,
I used VirSorter v2.1 on contigs from environmental metagenomes. I selected potential viral contigs with score >0.8. I then verify completeness with checkV. Several potential viral contigs whe…
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Hi Antonio,
I had a question about calibrated aggregated classification scores output by geNomad. If I run a metagenome assembly through genomad, would it be appropriate to use the calibrated aggre…
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Hi,
I was wondering whether you recommend to dereplicate and filter viral contigs identified by viral sorting tools like VIBRANT, VirSorter2, etc. before running PropagAtE or if you recommend to us…
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Hi Linxing:
Thank you for developing this nice tool! I am curious about what's the functions does COBRA have in the classic virome pipeline as it's a new software.
For example, I used MEGAHIT to get…