Fastq files containing more than one species

[Elsie]

Hi,

simple query with probably a simple answer, I've got some sequence files (FASTQ) that I know contain several species - definitely several virus species for a start. What is a good way to find out what what is in my files, just BLAST?
thanks.

[mikep]

Compile all the genomes that are present into a fasta file, build a bowtie index against it and then run bowtie (or do a similar thing for which ever mapper you prefer).

We've has success doing this looking for HPV in human samples...as an aside for HPV, RNAseq is a more accurate serotyper than serotyping.

[westerman]

mikep's answer is good ... if you know before-hand the genomes that are present. If not then taking a random 5000 or so reads and using BLAST should work.

[Elsie]

Thanks, useful comments. I found this post - http://www.cureffi.org/2013/01/25/al...viral-genomes/ which also addresses what I am after, the idea of compiling all the genomes together is an excellent one and exactly what I was after, results look good so far, thanks for your help.