Title |
Tentacle: distributed quantification of genes in metagenomes
|
---|---|
Published in |
Giga Science, September 2015
|
DOI | 10.1186/s13742-015-0078-1 |
Pubmed ID | |
Authors |
Fredrik Boulund, Anders Sjögren, Erik Kristiansson |
Abstract |
In metagenomics, microbial communities are sequenced at increasingly high resolution, generating datasets with billions of DNA fragments. Novel methods that can efficiently process the growing volumes of sequence data are necessary for the accurate analysis and interpretation of existing and upcoming metagenomes. Here we present Tentacle, which is a novel framework that uses distributed computational resources for gene quantification in metagenomes. Tentacle is implemented using a dynamic master-worker approach in which 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 Tentacle 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 the source code are freely available online at: http://bioinformatics.math.chalmers.se/tentacle. |
X Demographics
Geographical breakdown
Country | Count | As % |
---|---|---|
United States | 4 | 16% |
Germany | 4 | 16% |
Canada | 2 | 8% |
United Kingdom | 2 | 8% |
Spain | 1 | 4% |
Netherlands | 1 | 4% |
Finland | 1 | 4% |
France | 1 | 4% |
China | 1 | 4% |
Other | 1 | 4% |
Unknown | 7 | 28% |
Demographic breakdown
Type | Count | As % |
---|---|---|
Scientists | 16 | 64% |
Members of the public | 8 | 32% |
Science communicators (journalists, bloggers, editors) | 1 | 4% |
Mendeley readers
Geographical breakdown
Country | Count | As % |
---|---|---|
Brazil | 2 | 5% |
Ireland | 1 | 2% |
Sweden | 1 | 2% |
United Kingdom | 1 | 2% |
Japan | 1 | 2% |
United States | 1 | 2% |
Unknown | 37 | 84% |
Demographic breakdown
Readers by professional status | Count | As % |
---|---|---|
Student > Ph. D. Student | 11 | 25% |
Researcher | 10 | 23% |
Student > Bachelor | 7 | 16% |
Student > Master | 4 | 9% |
Student > Doctoral Student | 3 | 7% |
Other | 8 | 18% |
Unknown | 1 | 2% |
Readers by discipline | Count | As % |
---|---|---|
Agricultural and Biological Sciences | 17 | 39% |
Biochemistry, Genetics and Molecular Biology | 8 | 18% |
Computer Science | 6 | 14% |
Mathematics | 3 | 7% |
Immunology and Microbiology | 3 | 7% |
Other | 6 | 14% |
Unknown | 1 | 2% |