-
I am using starchip's fusion mode to detect integration sites between the host (human) and viral genomes that I know the host is infected with. To allow starchip to recognize the fusion pair between t…
Apb58 updated
5 years ago
-
@miparedes @cassiawag ---
Could you add two command line options to `extract_cluster_fastas.py`? These are:
* `--min-size`: Take a parameter for the minimum number of genomes to include in an outp…
trvrb updated
5 years ago
-
Dear Heyden,
I am quite interested in both CATCH and your paper on Nature Biotech (https://www.nature.com/articles/s41587-018-0006-x#MOESM3) as a method to define custom probes for viruses. CATCH i…
-
Hello, I have already build a custom database containing bacteria, virus and fungi. Unfortunately, I noticed that my database lack some representative genome...Is there a possibility to add some genom…
fetyj updated
5 years ago
-
Dear authors,
First of all, I have to say that kodoja is working perfectly for my purposes, really good job!
I would like to know whether there is a functionality that allows me to list or retri…
-
Dear all,
I am trying to run the CANU on my DATA and it keeps failing before assembly step (bogart failed). So I have corrected and trimmed data as the output. Anyway, I have directRNA data and I am …
-
I ran `PROKKA` and `Prodigal` (in an independent run) to detect CDS. The resulting `gff` file generated by `PROKKA` contains fewer than half the features than the `gff` file from `Prodigal`. I also ma…
-
Hello, I have an error, and not sure how to prevent it, or if this is an issue with the software itself.
Using canu version 1.8 on Ubuntu 16.04.6 LTS (no virtual machine).
```
$ canu --version
…
-
Hello professor,
i cannot figure out how to run prokka against online repositories. Instead im fetching genomes (using BLAST to assess similarity) by accession numbers:
fetch_genome_by_accession.s…
-
Currently, besides reference genomes, `select_strains.py` is only passing through viruses that possess both HA and NA segments (due to our use of `--segments ha na` in the snakefile). For time pivots …
trvrb updated
5 years ago