Denoising pyrosequencing reads by flowgram clustering

This page hosts the software described in our paper
Rapidly denoising pyrosequencing amplicon reads by exploiting rank-abundance distributions
published in Nature Methods, Volume: 7, Pages: 668-669 (2010)

We understand our program as a fast, heuristic alternative to Chris Quince's PyroNoise software suite (now called Amplicon noise). Chris introduced the concept of flowgram clustering and he deserves all the merits. If you are interested in this topic you might want to have a look at his paper Removing Noise From Pyrosequenced Amplicons BMC Bioinformatics 12:38.

The Denoiser has been fully integrated into the qiime 1.3 release and all new releases will only occur as part of qiime. Please check the Qiime website for the newest version.

The last stand-alone stable release of our software can be downloaded here:


This release contains updated error profiles for the Titanium sequencing platform using data published by S. Balzer and K. Malde in their 2010 Bioinformatics paper. We tested the new profile on one of the Mock communities the we used for our original publication sequenced on a Titanium machine. Our main findings from that analysis are:

  1. Denoising Titanium data with the older FLX profiles is less effective than denoising FLX data.
  2. Denoising with the new error profiles and slightly higher clustering thresholds (both can be simply set using the new --titanium switch) reduces the number of false OTUs considerably.
  3. Even after denoising, Titanium data seems to have more noise (and thus more false OTUs) than FLX data. Therefore, we suggest to use a very aggressive quality filtering (e.g. tight length bounds) prior to denosing to remove as many suspicious reads as possible. As a consequence, you should be very careful when directly comparing Titanium and FLX data, denoised or not.
As a side effect, the new version should usually run faster for most Titanium runs, since the runtime depends directly on the number of clusters.

See the included INSTALL file for installation help and the README for a quick tutorial. Also check the FAQ for some frequent problems.

Compatibility with QIIME:
The 0.91 release is compatible with the current stable Qiime release (1.2.1). However, in order to use the titanium switch from QIIME's wrapper script you will have to update to the current QIIME SVN version or wait for the next QIIME release.

Change log:

For questions or comments, please contact jens.reeder(at) or visit the QIIME forum

Last edited March 9th 2011.