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Old 11-17-2015, 02:21 PM   #1
ksw9
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Default Determine species composition in short-read data

Hi,
I am wondering the best approach for testing for contamination in short-read sequence data from host/environmental genomes which were not the target of the sequencing study. Specifically, I have mapped short read data to a reference genome and see an unexpected level of polymorphisms at the 16S locus. I would like to figure out if this variation is attributable to true biological variation, or potentially, if this variation is actually attributable to sequence reads from other contaminating genomes which map nevertheless to my reference genome of interest.

Thank you!
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Old 11-17-2015, 02:47 PM   #2
Brian Bushnell
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Try assembling and BLASTing the assembly against nt or refseq bacteria, and looking for hits in other taxa. Also, note that organisms will have multiple 16S copies that are not identical.
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Old 11-17-2015, 05:04 PM   #3
themerlin
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I know folks who use Kraken for this sort of thing.

https://ccb.jhu.edu/software/kraken/

Jason
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