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Old 02-10-2017, 12:31 PM   #9
David Eccles (gringer)
Location: Wellington, New Zealand

Join Date: May 2011
Posts: 836

For taxonomic surveys, you'd be better off doing a full metagenomic analysis instead of looking at specific genes. The MinION is more than adequate for this purpose.

Metrichor provides a WIMP ("What's In My Pot") workflow for doing exactly this. It uses Kraken* behind the scenes to vote on the origin of subsequences of each read, generating a consensus taxon for each read. The end result is a tree with counts that will show in real time (i.e. during sequencing) the content of your sample. The output using extracted, unamplified DNA correlates extremely well with the expected output for "canned" metagenomic samples:

* it used to use Kraken, but that may have changed with recent releases
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