-
It seems that "penalty" for soft clip, which is specified by the `-L` argument is "reward" rather than "penalty". More specicailly, given the example below:
reference file is
```
>ref
ACTGGCAT…
-
Hello again,
I closed the previous issue I was having as I feel we resolved this - the program ran now after I did a first assembly step to reduce the complexity of a full MGS file of raw data.
No…
-
Hello.
I am using Ubuntu and I have tried python versions 3.5, 3.7, 3.9, and 2.7 and each time I get an error that my python version is wrong. I have tried to create a clean environment using: conda …
mr249 updated
11 months ago
-
Hi!
Thanks a lot for developing this useful tool! I am currently trying to run it on a set of ~2,000 viral genomes.
I followed the GitHub instructions and:
- I also added prodigal to the path (…
-
Hi, I am trying to create synteny between phages.
###upload files
s0
-
Hi Katelyn,
thanks for PHANOTATE, great tool!
I'm using it for larger sets of viral contigs, and noticed that it seems to not free up RAM between contigs. On my current set with 100+ sequence, t…
-
Hello,
First of all again, many thanks for developing this great tool. I open this issue because I wanted to know which probability cutoff is recomended, in your opinion, as a minimum to trust a 3…
-
====
- (mostly . . . allow exons to overlap), just for specific isoforms
====
as @cmdcolin noted, we have a bunch of code for frameshifts and they are in the code, but we do not appear to act…
-
Hi,
thanks for making this available it seems like a very useful pipeline. The last few days I tested it a bit, mainly for running viral classification and wanted to share some issues I encountered.…
-
Hi!
First of all, thank you for putting together such a nice pipeline! It's very convenient to have all of these tools in one place.
I installed BEAV using conda as per instruction on the readme…