-
Hello
I have been trying to run the bactopia pipeline from the singularity (supported in my cluster) container pulled from `quay.io`.
I managed to download the datasets, which worked onl…
-
Hi Rob,
I am using Bactopia v2.0.3, running the command "bactopia --fastqs fastqs.txt --datasets datasets/ --species "Klebsiella pneumoniae" --coverage 100 --nfconfig /mnt/isilon/bactopia_respub…
-
Hello Theiagen Team,
I'm performing SNP and phylogenetic analysis for a set of bacterial samples on Terra using PHB v1.0.1. When I compared the core genome SNP matrix output from the kSNP3 workflow…
-
I will collect the ToDos from this thread here @GwennyGit maybe you can mark what you did already and on what branch :D
- [x] remove CGXII and replace by CGXlab but rename to CGXII
- [x] remove LB an…
-
Hello!
First I want to say thank you for maintaining this awesome software :)
I have a question regarding the input VCF format when using snpgenie.pl.
For context, I am interested in analyzi…
-
**Description**
I was trying to launch a Bactopia run using nf-tower. From the schema it expects `R1` and `R2` parameters:
https://github.com/bactopia/bactopia/blob/89885c5dd9824ac6540ca10becc138876…
-
**Describe the bug**
Depositing some bacterial genomes, I noticed that 9 of them come back with a /pseudo tag on the dnaA gene after PGAP annotation. They all have this field
/…
-
Greetings! Firstly, I would like to express my sincere gratitude for your dedicated efforts in developing the MGEfinder software. Your work has greatly facilitated our research endeavors.
I am curr…
-
Hi,
1. When i used contigs file, no result obtained.
2. But when a subset was made and used for analysis then following result obtained.
3. But No data in warnings folder.
Pls suggest.
Thanks
…
-
Hi, I encounter the same problem as in https://github.com/facebookresearch/LAMA/issues/10.
And I found the reason why 2 examples are filtered is that the `obj_label` are `1970s` and `1990s`. And in `…