Will qiime2 support functional gene analysis in the future?

[colinbrislawn (Colin J Brislawn)]

Qiime2 is not specific to 16S! It can work on any gene targeted with PCR right now, including functional genes.

Here's Nick's summary of the process:

Working on functional gene- providing a database

QIIME 2 is not specific to rRNA genes… many users commonly use other coding and non-coding marker genes, e.g., COI, ITS, even some functional genes like nifH, etc. You need to find or construct this database, e.g., by compiling known reference genes. That database will need to be formatted the same way as other databases that are commonly used by QIIME 2 — so take a look at the greengenes or SILVA reference database to get an idea of what these formats are (fasta sequences and tab-delimited, …

So basically, you can follow the same pipeline for 16S amplicons, and just a custom database at the taxonomy assignment step.

Colin