Which version NCBI nt database is recommenced for a plant genome

DRL / blobtools

Modular command-line solution for visualisation, quality control and taxonomic partitioning of genome datasets

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Which version NCBI nt database is recommenced for a plant genome #71

Closed drashutosh closed 6 years ago

drashutosh commented 6 years ago

Hi Dom I am working on a plant genome and intended to use blobtools as one of the filtering steps in my pipeline. So far I did some blast run using NCBI nt database and produced blobplots for those run. I used nt. 26 as a random database in my blast search.

It is 57 nt databaseversion in the ftp://ftp.ncbi.nlm.nih.gov/blast/db/

What version would suggest to use for getting better results with blobtools?

Thanks in advance

Ashuttosh

DRL commented 6 years ago

Hi Ashuttosh,

if you want to blast against NCBI nt, you need to download all 58 files (nt.00.tar.gz - nt.57.tar.gz) for the pre-formatted blast database. The individual files are not versions, but parts of the same database.

hope that helps,

dom