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Hello, currently, i want to identity the viral sequences with length > 1000, but phigaro seems to automatically exclude sequences with length < 20000. If i don't add the option "-d", it will prompt m…
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Hi!
I am using WTP with a very large input file of contigs (10,977,373 seq)
**Command used:** nextflow run replikation/What_the_Phage --fasta all_contigs_Champ_2016_2020.fa --cores 12 -r v1.0.2…
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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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Hi ,
I get the following error 👍
`Error executing process > 'bacannot_nf:digis (Scanning for Insertion Sequences with digIS)'
See shot below:
`
![image](https://user-images.githubusercontent.…
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Hi Polly,
I was trying to download the pvog database to setup phigaro but this link is not working (http://download.ripcm.com/phigaro/).
Is there another way to download pvog and setup phigaro?
…
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Nice tool and idea. Perhaps our phigaro tool could also be included (although I appreciate that adding new tools is probably not trivial):
https://academic.oup.com/bioinformatics/article/36/12/3882/5…
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Hi,
I use the following command to run wtp with an input fasta file (~60M):
`nextflow run replikation/What_the_Phage --fasta wtp/all_combined.fasta --databases nextflow-autodownload-databases --ca…
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README says:
Proper prophage detection is not implemented (yet) - but a handful of tools report them - so they are mostly identified
What are those tools, other than phigaro? What programs contrib…
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Some issues have been identified in the latest release! The main problems are in phigaro and jbrowse processes (I have detected a few problems with conditionals and output parameters for these).
Th…
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(phigaro) ➜ ~ sudo phigaro-setup
sudo: phigaro-setup: command not found