checkV

[ntromas]

Hi,

First of all, thanks for this pipeline! I wonder what would be the best approach to deal with checkV once we have the best bins and used the script link_bin_sequences.py. CheckV is using Prodigal but it is not possible (to my knowledge) to add the -m option.

Thanks!

Nico

[KrisKieft]

Hi,

This is a great question and something I have been thinking about myself. Unfortunately, since binning is "new" for viruses there isn't universal bioinformatics infrastructure set up for handling bins. I did notice that the CheckV output will generate proteins with strings of Xs corresponding to Prodigal not running the -m option. I actually went into the CheckV code myself and added -m to the Prodigal call for my own research, though I'm not going to share that code because it's not my tool. It may be worth contacting Stephen Nayfach (lead author on CheckV) for a solution to this. He's a great guy and active member in the scientific community, so he should get back to you with some options for CheckV.

Let me know if you have any more questions on this. As a side note, vConTACT2 can handle bins by setting up the gene-to-genome.csv file accordingly.

Kris

[ntromas]

Hi Kris,

Thanks for the detailed information! I will write him to ask. I am for now exploring vRhyme but will have other questions for sure. Thanks again for the pipeline!

Nico

[bio-shun]

I had the same problem, but I looked at the checkv（ https://bitbucket.org/berkeleylab/checkv/src/master/checkv/utility.py ）The utility.py code of shows:

def run_ prodigal(out): cmd = "prodigal-gv " cmd += " -m " cmd += "-p meta "

Does it mean that the author has added the - m option?

[KrisKieft]

Please contact appropriate authors or Issues pages for other software. But yes, this code appears to add the -m flag.

[bio-shun]

Please contact appropriate authors or Issues pages for other software. But yes, this code appears to add the -m flag.

thanks for your excellent pipeline！