FOCUS, an innovative and agile composition based using non-negative least squares to profile and report abundant organisms present in me-tagenomic samples and their relative abundance without sequence length dependencies. The program was tested with simulated and real metagenomes, and the results show that our approach predicts the organisms in random communities.

Availability and implementation: The code implemented in Python can be found here and a web-sever at http://edwards.sdsu.edu/FOCUS.

Dependencies: Jellyfish, Numpy, and Scipy.

Cite FOCUS

Silva, G. G. Z., D. A. Cuevas, B. E. Dutilh, and R. A. Edwards, 2014: FOCUS: an alignment-free model to identify organisms in metagenomes using non-negative least squares. PeerJ, 2, e425,doi:10.7717/peerj.425.

Features

  • Metagenomes
  • Richness
  • Evenness

Project Samples

Genera-level taxonomy classification sorted by FOCUS prediction for the metagenome from a diseased human oral cavity using FOCUS, MetaPhlAn, MG-RAST, PhymnBL, RAIphy, Taxy, and FOCUS (mean). Error bars represent the standard deviation uncertainty in tested metagenome Scalability test using different sub-sets of the human oral cavity under disease metagenome using FOCUS, MetaPhlAn, MG-RAST, PhymnBL, RAIphy, Taxy Genera-level taxonomy classification sorted by FOCUS prediction for the metagenome from a health human oral cavity using FOCUS, MetaPhlAn, MG-RAST, PhymnBL, RAIphy, Taxy, and FOCUS (mean). Error bars show the standard deviation uncertainty for the real metagenome. Genera-level taxonomy classification for the SimShort dataset using FOCUS, PhymnBL, RAIphy, and FOCUS (mean). Class-level taxonomy classification for the SimHC dataset using FOCUS, PhymnBL, RAIphy, and FOCUS (mean) Workflow of the FOCUS program

Project Activity

See All Activity >

Follow FOCUS

FOCUS Web Site

Other Useful Business Software
MongoDB Atlas runs apps anywhere Icon
MongoDB Atlas runs apps anywhere

Deploy in 115+ regions with the modern database for every enterprise.

MongoDB Atlas gives you the freedom to build and run modern applications anywhere—across AWS, Azure, and Google Cloud. With global availability in over 115 regions, Atlas lets you deploy close to your users, meet compliance needs, and scale with confidence across any geography.
Start Free
Rate This Project
Login To Rate This Project

User Reviews

Be the first to post a review of FOCUS!

Additional Project Details

Registered

2013-06-29
Report inappropriate content