Supporting materials and software for "Tentacle: distributed quantification of genes in metagenomes".

In metagenomics, microbial communities are sequenced at increasingly high resolution generating data sets with billions of DNA fragments. Novel methods that can efficiently process the growing volumes of sequence data are necessary for accurate analysis and interpretation of existing and upcoming metagenomes. Here we present Tentacle, a novel framework which uses distributed computational resources for gene quantification in metagenomes. Tentacle is implemented using a dynamic master-worker approach where DNA fragments are streamed via a network and processed in parallel on worker nodes. Tentacle is modular, extensible, and comes with support for six commonly used sequence aligners. It is easy to adapt to different applications in metagenomics and easy to integrate into existing workflows. Evaluations show that Tentacle scales very well with increasing computing resources. We illustrate the versatility of Tentacle on three different use cases. Tentacle is written for Linux in Python 2.7 and is published as open source under the GNU General Public License (v3). Documentation, tutorials, installation instructions, and source code is freely available online at: http://bioinformatics.math.chalmers.se/tentacle.

Keywords:

• distributed computing
• metagenomics
• gene quantification
• DNA sequence analysis
• read mapping

Read the peer-reviewed publication(s):

• Boulund, F., Sjögren, A., & Kristiansson, E. (2015). Tentacle: distributed quantification of genes in metagenomes. GigaScience, 4(1). https://doi.org/10.1186/s13742-015-0078-1

Additional information:

http://bioinformatics.math.chalmers.se/tentacle/

http://figshare.com/articles/Tentacle_quantification_accuracy_evaluation/1403609

https://bitbucket.org/chalmersmathbioinformatics/tentacle