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I just run the nextflow pipeline again using `v0.3.0` on the `~/.nextflow/assets/EBI-Metagenomics/emg-viral-pipeline/nextflow/test/kleiner_virome_2015.fasta` example data set.
Now, the pipeline on…
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This isn't really an issue but more of a question about the uses of the RagTag scaffold function.
I want to monitor prophage movement in clonal isolates, but only have access to short read data an…
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Hello,
According to the `checkv.nf` there are several calls to checkv's functionality. However, I am only getting the final summary stats for quality in the `_contigs_quality_summary.tsv` .
The …
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Dear WTP team,
Thanks for this excellent pipeline!
I played a bit with my dataset and I got 86 viral positive contigs. However, the output from checkV only found very few with viral gene. Is check…
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Hello Mike,
I'm using Cenote-Taker2 to discover viral elements in my samples. I'm really glad that there are lots of viral genes are identified but I have two questions and hope to have you suggest…
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I'm currently using version 1.2.1 to analyze metagenomic assembly data. I completed my analysis on one sample and identified 17 phages from 720 contigs with run_vibrant.py. It looks like everything w…
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Hi Simon,
I have installed VirSorter but I am getting this error when running:
`/srv/scratch/z3336178/anaconda/envs/virsorter/bin/blastp: error while loading shared libraries: libssl.so.1.0.0: c…
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Hello
As a result, phigaro gives out various fields such as taxonomy, transposable, VOG, et cetera for each prophage found. Is there any way to get the intact or defective status using that informa…
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Hello,
I have trying out VIBRANT lately and although I find it is superbly made, I have run into a couple of issues regarding prophage identification. As a test, I have input the whole genomes from…
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I am running VIBRANT on virome samples with the "-virome" flag added to my runs. I have all of the expected output files except for the VIBRANT_integrated_prophage_coordinates_{sample}.tsv in the VIBR…