Illumina HiSeq2500 metagenome Sequencing chimera

Question

[Phil S.]

Hi all,

I know chimeras are a problem using 454 amplicon sequencing. I wonder if this is also possible using Illumina sequencing (and there the nextera (xt)) kit. If so, are there any recommendations of getting rid of those sequences. I don't want to assemble the reads to identify them (if this is possible).

Thanks for your thoughts / suggestions!

Phil

Answer 1

[lelle]

If you are producing amplicons there will always be a certain risk to produce chimeras during the PCR amplification. The sequencing technology that you use afterwards is pretty much irrelevant.

I think the ideal way to detect chimeras is to do replicates (of the amplification step) and work with the assumption that is is very unlikely to have the same chimeras in both of them.

You can also do in silico chimera detection (for example with UCHIME).

[Phil S.]

Actually we are doing both ways of metagenomics, by that I mean amplicon and shotgun sequencing. I will have a look into UCHIME for sure! Thank you!