Curate a specific Reference Database only containing species/strains belonging to one bacterial family

Question

[Raphaela]

Hi all,

for my latest research project I am planning to analyse faecal samples for the presence and abundance of Lactobacillaceae species/strains, which in turn will be used to associate with lipid profiles in cardiovascular disease.

As I am solely interested in the presence of microbes belonging to the family of Lactobacillaceae, I am looking for a R package or similar relevant tool which facilitates the creation of an individually setup reference data base.

I tried the R function metaretrieval (as included in the biomartr package https://github.com/ropensci/biomartr), which allows the retrieval of reference genomes from the NCBI databank, however it only allows subsetting up to phylum level, whereas I want to collect all microbes belonging to a family of bacteria.

Has anybody got any experience, advice or other hints on where to go from here?

Grateful for any support on this matter. Thanks in advance!

Answer 1

[GenoMax]

You can use the following tools to download the genomes you need:

• Genome updater (LINK)
• NCBI genome download (LINK)

Take a look at the GitHub help pages to find exact option you need. Once you get the .fna files (nucleotide sequence) or .faa files (protein sequence) you can build your custom database for blast+ or DIAMOND.