-
Hi,
I am just starting to use your package. I have list of bacteria I would like to look for in my samples. However, I did a test with a small test following the tutorial and found that the sapply f…
-
I am currently implementing NCBI taxonomy in CoNekT Grasses Microbiome. I believe this is something we should keep synchronized (Plant Cell Wall Knowledgebase, PAGED and CoNekT Grasses Microbiome). @…
-
-
This may be a duplicate but I haven't found it yet
```YAML
host_taxid:
has_raw_value: Brachypodium distachyon [NCBI:txid15368]
term:
id: NCBI:txid15368
name: Brachypodium…
-
Hi,
I tried to run this command with block size 1M from wiki:
`parallel -k --pipepart -a prot.accession2taxid --block 100M fgrep -F -f RVDB-prot.id.txt | cut -f 2,3 > RVDB-prot.taxonId.txt`
The…
-
**Describe the bug**
I am using the most recent version
```
datasets --version
datasets version: 16.33.0
```
When I down…
-
Currently, the pipeline uses NCBI's `rankedlineage.dmp` taxdump file for taxonomic standardisation, which only has the ranks `kingdom`, `phylum`, `class`, `order`, `family`, `genus` and `species`. How…
-
I would suggest rebuild metabuli viral reference database using current official viral taxonomy provided on https://ictv.global/vmr
Technically, it is not difficult.
Your tool processed it very smo…
-
NCBI is the authority, we should resolve there (just as PR resolves to the PRO website, GO to AmiGO, HPO to HPO/Monarch, etc).
E.g.
https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=9606
-
Hello Avil;
I'm having some issues while running:
`kdb --db-type standard --threads 24 --cache-dir --no-check-certificate`
And I got
`Traceback (most recent call last):
File "/usr/lib/p…