Dear all,

I am working on the data analysis of environmental sequences obtained by an Illumina MiSeq platform. Since the automatic checks for the presence of chimeric sequences did not remove all chimeric sequences, I want to check manually for the presence of extra chimeric sequences in the unclassified OTUs.

I reasoned that chimeric sequences in BLAST should give multiple independent hits from different species, showing a 'broken' alignment against the reference sequences. However, I have the feeling that this sometimes also happens for 'good OTUs'. So, does anyone have experience with using BLAST for this issue? How reliable is BLAST in this case?

Thanks!

Eveline