-
What I see is that NCBI Taxonomy has now
Keenocardium californiense
Taxonomy ID: 1421200 (for references in articles please use NCBI:txid1421200)
current name
Keenocardium californiense (Deshay…
-
# Script
db="ncbi_nt/ncbi_nt"
kma -ipe A16_S5_3_F22_S139_R1_001.atria.fastq.gz A16_S5_3_F22_S139_R2_001.atria.fastq.gz -o A16_S5_3_F22_S139_out_kma -t_db $db -t 20 -1t1 -mem_mode -and -apm f
# …
-
Hello,
When running both ./updateTaxonomy.sh and ./updateAccessions.sh I encounter the following error:
molbio@CLCServer:/MolbioDataDrive/Scripts/KronaTools-2.7.1$ ./updateTaxonomy.sh
Fetching …
-
Hi,
I want to create a Kraken2 DB with GTDB data, since it's so much more curated and reliable than NCBI. However, I do need to be able to detect all domains of life, so I want to include NCBI's fu…
-
Hi,
I'm trying to use this tool but it's unclear where the names and nodes files comes from in the documentation.
```
$ metaDMG config raw_data/alignment.sorted.bam \
--names raw_data/names-mdm…
-
Hello,
Thanks for this nice tool
I am trying to apply the method on 16S fastq. The taxonomy sequence for bacteria could be downloaded from NCBI however I don't understand
1- which .dmp file …
-
I'm trying to use a clustered version of the NR database for taxonomy assignment but am running into some issues. Any assistance would be appreciated.
## Expected Behavior
When running `mmseqs cre…
-
Hello!
I have used diamond to obtain hits with public databases and then filtered my data using Blobtools. I have used the commands specified on your webpage (https://blobtoolkit.genomehubs.org/blo…
-
Hi,
I have tried the add taxonomy step multiple different ways and it doesn't seem to work, even though no errors are reported.
`blobtools add --hits Coemansia_sp._RSA_376.ncbi.blastn.out --hits…
-
Implement parser and integrate it with code for storing data in DynamoDb