How to performe an "Exhaustive" search for contaminants

[Matthew Oldach]

Most of the time the contaminating species are known ahead of time and used for database(s) assembly.

I would like to use DeconSeq to remove contaminants from human WGS data derived from Saliva.

I started out by downloading the Human Oral Microbiome Database (HOMD) and testing this out on a proband first. There are ~1,900 genomes here resulting in 4.0Gb FASTA file which needed to be split in order to build indexs with BWA.  Now, I would like to perform a more exhaustive search for contaminants, including those which may not be known beforehand.

What is the best way of doing this? Is there a FASTA file somewhere which has all of the known genomes (I could then subset by removing human and search for everything else).

[Matthew Oldach]

The correct answer is to go to NCBIs RefSeq Genomes and follow their readme for how to download.