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Microbiome profiling software for 16S/18S/ITS rRNA gene dataty

Microbiome profiling of amplicon data is performed using BION where applicable. BION is open-source (with restriction on commercial usage) [BION software] exclusively written by [Danish Genome Institute], Aarhus, Denmark.


BION does all the basic processing for amplicon reads: cleaning, joining, filtering, de-replication, clustering, chimera checking and similarity matching, and finally creates organism abundance profiles.

We believe BION is more accurate than other packages. The main reasons for that are:

Better profiling logic.

Similarities are processed by a two-pass logic where highly similar alternative reference taxa are being chosen by their relative similarities.


This usually results in reliable mapping at the species level rather than genus, provided the sequences are of a good length and quality.

Cleaner sample data.

Through small tweaks of the logic behind each step, the sequences that reach the similarity mapper have optimal quality.


For example the clustering logic prefers the highest quality sequences as cluster center and only these are then similarity-matched.

Cleaner reference data.

We post-process reference data through a number of steps which in combination reduce false positive and negative matches (the “bogusphere”).


We plan to harvest and distribute our own reference sequences from the primary databanks in response to growing demand.

Data restrictions: At the moment BION can only process SSU RNA and ITS data, either paired or single.

BION is a software under constant improvement and maintenance, and our close collaboration with the Danish Genome Institute ensures that the software is customized to your specific data. The Danish Genome Institute plan to harvest and distribute their own reference sequences from the primary databanks in response to growing demand, thereby ensuring up-to-date reference data.

To facilitate an open and communicative service, we provide a downloadable description of the logic behind all steps, a 1-page feature summary sheet, a typical results archive, an abundance table in HTML form (made from 16S rRNA V3-V4 samples with known content), and the whole code archive for the version currently used in our services. Please contact us to have these documents and files provided.

Free reruns as reference data improves. If your data is of good quality and you let it stay on our servers, then we will rerun it with new methods as they appear, against better reference data as they become available, all at no cost.

The NGS-based microbiome field is in early stages and new organisms are constantly identified and/or known organisms are regrouped.


As a consequence, it can often be meaningful to re-analyse  data at later time points.  In exchange for the free re-runs, you allow us to make internal use of this (anonymized) data as a way to improve our service for other clients.

Local installation of the BION software

In addition to our online service for data processing and analysis, we offer to support you with a local installation of the BION package into your existing infrastructure. This option may be ideal if you routinely work with amplicon data and would like to process the data in-house, without having to deal with software installation or maintenance.


We offer to help with the installation (remotely through screensharing and Skype communication) and then help to write a workflow “guide” that fits your input data and get the first data through. The local installation is offered via The Danish Genome Institute , who also have service subscriptions for those who want our help any time needed.