How to separate eukaryotic sequence reads from my metagenome data?

[SaiPrabhas]

Hello!

I have Illumina Hiseq data from leafhopper Empoasca fabae. It has two symbionts, Sulcia muelleri, and Nasuia deltocephalinicola. In my project, we sequenced head and bacteriome regions of 4 different leafhopper specimens. We want to know if they are any differences in bacterial populations between these specimens and also want to see if they are any new bacteria present in the head samples of leafhopper. As the genome of the leafhopper is not sequenced yet, I cannot map the reads to a reference genome and filter out the eukaryotic reads so that I can analyze the bacterial population. How can I solve this problem? Thank you very much.

Regards,
Sai

[GenoMax]

Want to make you aware of BBSplit from BBMap.

Following is not completely thought through so take with a grain of salt.

There seem to be too many unknowns in this design to be able to use BBsplit directly. You could bbsplit all samples against each other to see if you can get as much of the leafhopper out as you can but it is going to take out some of the common bacteria as well.

Is there a related genome (to leafhopper) available? That would be the second best bet.

[WhatsOEver]

1) bacteria often have a higher GC-content than eukaryots, so this might be a starting point
2) You could filter your dataset for the known symbionts (which genomes are available, at least acc to a 5s google research) and try an assembly with the rest (depending on what this Hiseq data is: WGS/RNA-Seq?)
3) If you could get a collection of genomes of known insect symbionts, try merging all these and map against this set
4) Contact the people belonging to the abstract "Hybrid De Novo Assembly of the Leafhopper Genome with SMRT Sequencing Method" I also found via google