Annotating a contig and bacterial or eukaryotic (contamination screening)?

[kmkocot]

Hi all,

We are sequencing the genome of a microscopic invertebrate. Our assembly has significant bacterial contamination that we would like to remove prior to gene modelling. Is anyone aware of a publicly available tool that includes diverse bacterial genomes as references that I could use to annotate my contigs as either bacterial or eukaryotic?

Thanks!
Kevin

[GenoMax]

BBSplit was designed for separating reads into pools so you can enrich reads of potential interest (http://seqanswers.com/forums/showthread.php?t=41288). Only problem in your case is you don't know which bacterial species you should be screening against. If you have a rough idea you could select a representative set of genomes and start there.

If a close(r) relative of the microscopic invertebrate has had its genome sequenced then you could use that as the "bait" to fish out reads that would represent things of interest to you.

[kmkocot]

Thanks! This was not on my radar but should be very helpful!

Best,
Kevin