checkV output

[ntromas]

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 checkV too conservative?

My second question concerns the prophage prediction, is there a way to separate potential viral contigs to potential prophage contigs?

Thanks!

Nico

[mult1fractal]

Hey @ntromas Thanks for the positive feedback!

1) We are running CheckV with default settings... but if you want to use different settings you can also use the docker container nanozoo/checkv:0.6.0--e97f45e but make sure you start the container in the folder where the checkV database is located... or mount the database into the docker container.

2) We are currently working on a scoring system (probably in august as new release)... I will put your suggestion on my to do 👍🏽 but for now: using the raw output from checkV

• via grep: get rows that are of interest for you (eg rows/contigs that are potential prophages)
• extract contig_names
• via samtools: extract sequences from your input based on the extracted contig_names (you can use the samtools docker if you don't want to install samtools on your PC nanozoo/samtools:1.9--76b9270)

Hope it helps!

Mike