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Hi! I have been using Kaiju for a while, and now I am interested in filtering fungal reads. For this, I used the Kaiju app in KBase and compared the results using two different databases: NCBI BLAST n…
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todo:
- [x] port to python 3
- [x] test suite (pytest)
- [x] build conda package
- [x] build pypi package
- [x] set up builds on appveyor and circleci for win and linux builds of conda packages…
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I'm doing a standard Cas9 search on a 1 gigabase chicken genome and the step "Find genomic features closest to the guide" is taking longer than the guide finding step. I ran this on a 384 GB, 48-core…
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Hello
Could you please help me to run your pipeline? I only have one gene that I would like to find its orthologs in 136 sequenced plant genomes.
Do I need to download the sequenced genomes (in …
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Hallo,
I have some questions about the use of Phylophlan as phylogenetic analysis for microbial isolates/genomes :
- Is it correct to use Phylophlan for detecting persistent strains ?
- How d…
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Hi,
I am trying to annotate 12 microbial genomes using MA installed at HPC (slurum), (using blast). following are the current options I am using, but it's been running for days, I was wondering if…
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Dear Simon,
I've been running VirSorter on the cyverse platform before, and now installed it on a server (CentOS Linux 7), as I'd like to use it for a larger number of samples. I followed the insta…
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**Dataset title**
Genome Taxonomy Database (GTDB)
**Dataset contact & access**
https://gtdb.ecogenomic.org/
https://data.ace.uq.edu.au/public/gtdb/data/releases/latest/ar122_taxonomy.tsv
https:…
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This issue can serve as a placeholder for use cases for sourmash/MinHash more generally.
Stuff we already have implemented:
* basic MinHash comparisons etc
* metagenome taxonomy breakdown
* st…