title: SEK: sparsity exploiting k-mer-based estimation of bacterial community composition.
abstract: BACKGROUND
  Estimation of bacterial community composition from a high-throughput sequenced sample is an important task in metagenomics applications. As the sample sequence data typically harbors reads of variable lengths and different levels of biological and technical noise, accurate statistical analysis of such data is challenging. Currently popular estimation methods are typically time-consuming in a desktop computing environment.
  
  
  RESULTS
  Using sparsity enforcing methods from the general sparse signal processing field (such as compressed sensing), we derive a solution to the community composition estimation problem by a simultaneous assignment of all sample reads to a pre-processed reference database. A general statistical model based on kernel density estimation techniques is introduced for the assignment task, and the model solution is obtained using convex optimization tools. Further, we design a greedy algorithm solution for a fast solution. Our approach offers a reasonably fast community composition estimation method, which is shown to be more robust to input data variation than a recently introduced related method.
  
  
  METHODS
  A platform-independent Matlab implementation of the method is freely available at http://www.ee.kth.se/ctsoftware; source code that does not require access to Matlab is currently being tested and will be made available later through the above Web site.
authors.affiliation: Department of Communication Theory, KTH Royal Institute of Technology, Stockholm, Sweden, Department of Mathematics, Oregon State University, Corvallis, OR, USA, Systems Biology program, KTH Royal Institute of Technology, Sweden, Aalto University, Esbo, Finland, Department of Computational Biology, KTH Royal Institute of Technology, Stockholm, Sweden, Department of Mathematics and Statistics, University of Helsinki, Helsinki, Finland, Department of Physics, Tsinghua University, Beijing, China, Department of Signal Processing and Department of Information and Computer Science, Aalto University, Esbo, Finland.
authors.forename: Saikat
authors.initials: S
authors.lastname: Chatterjee
authors.affiliation: Department of Communication Theory, KTH Royal Institute of Technology, Stockholm, Sweden, Department of Mathematics, Oregon State University, Corvallis, OR, USA, Systems Biology program, KTH Royal Institute of Technology, Sweden, Aalto University, Esbo, Finland, Department of Computational Biology, KTH Royal Institute of Technology, Stockholm, Sweden, Department of Mathematics and Statistics, University of Helsinki, Helsinki, Finland, Department of Physics, Tsinghua University, Beijing, China, Department of Signal Processing and Department of Information and Computer Science, Aalto University, Esbo, Finland.
authors.forename: David
authors.initials: D
authors.lastname: Koslicki
authors.affiliation: Department of Communication Theory, KTH Royal Institute of Technology, Stockholm, Sweden, Department of Mathematics, Oregon State University, Corvallis, OR, USA, Systems Biology program, KTH Royal Institute of Technology, Sweden, Aalto University, Esbo, Finland, Department of Computational Biology, KTH Royal Institute of Technology, Stockholm, Sweden, Department of Mathematics and Statistics, University of Helsinki, Helsinki, Finland, Department of Physics, Tsinghua University, Beijing, China, Department of Signal Processing and Department of Information and Computer Science, Aalto University, Esbo, Finland Department of Communication Theory, KTH Royal Institute of Technology, Stockholm, Sweden, Department of Mathematics, Oregon State University, Corvallis, OR, USA, Systems Biology program, KTH Royal Institute of Technology, Sweden, Aalto University, Esbo, Finland, Department of Computational Biology, KTH Royal Institute of Technology, Stockholm, Sweden, Department of Mathematics and Statistics, University of Helsinki, Helsinki, Finland, Department of Physics, Tsinghua University, Beijing, China, Department of Signal Processing and Department of Information and Computer Science, Aalto University, Esbo, Finland.
authors.forename: Siyuan
authors.initials: S
authors.lastname: Dong
authors.affiliation: Department of Communication Theory, KTH Royal Institute of Technology, Stockholm, Sweden, Department of Mathematics, Oregon State University, Corvallis, OR, USA, Systems Biology program, KTH Royal Institute of Technology, Sweden, Aalto University, Esbo, Finland, Department of Computational Biology, KTH Royal Institute of Technology, Stockholm, Sweden, Department of Mathematics and Statistics, University of Helsinki, Helsinki, Finland, Department of Physics, Tsinghua University, Beijing, China, Department of Signal Processing and Department of Information and Computer Science, Aalto University, Esbo, Finland.
authors.forename: Nicolas
authors.initials: N
authors.lastname: Innocenti
authors.affiliation: Department of Communication Theory, KTH Royal Institute of Technology, Stockholm, Sweden, Department of Mathematics, Oregon State University, Corvallis, OR, USA, Systems Biology program, KTH Royal Institute of Technology, Sweden, Aalto University, Esbo, Finland, Department of Computational Biology, KTH Royal Institute of Technology, Stockholm, Sweden, Department of Mathematics and Statistics, University of Helsinki, Helsinki, Finland, Department of Physics, Tsinghua University, Beijing, China, Department of Signal Processing and Department of Information and Computer Science, Aalto University, Esbo, Finland.
authors.forename: Lu
authors.initials: L
authors.lastname: Cheng
authors.affiliation: Department of Communication Theory, KTH Royal Institute of Technology, Stockholm, Sweden, Department of Mathematics, Oregon State University, Corvallis, OR, USA, Systems Biology program, KTH Royal Institute of Technology, Sweden, Aalto University, Esbo, Finland, Department of Computational Biology, KTH Royal Institute of Technology, Stockholm, Sweden, Department of Mathematics and Statistics, University of Helsinki, Helsinki, Finland, Department of Physics, Tsinghua University, Beijing, China, Department of Signal Processing and Department of Information and Computer Science, Aalto University, Esbo, Finland.
authors.forename: Yueheng
authors.initials: Y
authors.lastname: Lan
authors.affiliation: Department of Communication Theory, KTH Royal Institute of Technology, Stockholm, Sweden, Department of Mathematics, Oregon State University, Corvallis, OR, USA, Systems Biology program, KTH Royal Institute of Technology, Sweden, Aalto University, Esbo, Finland, Department of Computational Biology, KTH Royal Institute of Technology, Stockholm, Sweden, Department of Mathematics and Statistics, University of Helsinki, Helsinki, Finland, Department of Physics, Tsinghua University, Beijing, China, Department of Signal Processing and Department of Information and Computer Science, Aalto University, Esbo, Finland Department of Communication Theory, KTH Royal Institute of Technology, Stockholm, Sweden, Department of Mathematics, Oregon State University, Corvallis, OR, USA, Systems Biology program, KTH Royal Institute of Technology, Sweden, Aalto University, Esbo, Finland, Department of Computational Biology, KTH Royal Institute of Technology, Stockholm, Sweden, Department of Mathematics and Statistics, University of Helsinki, Helsinki, Finland, Department of Physics, Tsinghua University, Beijing, China, Department of Signal Processing and Department of Information and Computer Science, Aalto University, Esbo, Finland.
authors.forename: Mikko
authors.initials: M
authors.lastname: Vehkaperä
authors.affiliation: Department of Communication Theory, KTH Royal Institute of Technology, Stockholm, Sweden, Department of Mathematics, Oregon State University, Corvallis, OR, USA, Systems Biology program, KTH Royal Institute of Technology, Sweden, Aalto University, Esbo, Finland, Department of Computational Biology, KTH Royal Institute of Technology, Stockholm, Sweden, Department of Mathematics and Statistics, University of Helsinki, Helsinki, Finland, Department of Physics, Tsinghua University, Beijing, China, Department of Signal Processing and Department of Information and Computer Science, Aalto University, Esbo, Finland.
authors.forename: Mikael
authors.initials: M
authors.lastname: Skoglund
authors.affiliation: Department of Communication Theory, KTH Royal Institute of Technology, Stockholm, Sweden, Department of Mathematics, Oregon State University, Corvallis, OR, USA, Systems Biology program, KTH Royal Institute of Technology, Sweden, Aalto University, Esbo, Finland, Department of Computational Biology, KTH Royal Institute of Technology, Stockholm, Sweden, Department of Mathematics and Statistics, University of Helsinki, Helsinki, Finland, Department of Physics, Tsinghua University, Beijing, China, Department of Signal Processing and Department of Information and Computer Science, Aalto University, Esbo, Finland.
authors.forename: Lars K
authors.initials: LK
authors.lastname: Rasmussen
authors.affiliation: Department of Communication Theory, KTH Royal Institute of Technology, Stockholm, Sweden, Department of Mathematics, Oregon State University, Corvallis, OR, USA, Systems Biology program, KTH Royal Institute of Technology, Sweden, Aalto University, Esbo, Finland, Department of Computational Biology, KTH Royal Institute of Technology, Stockholm, Sweden, Department of Mathematics and Statistics, University of Helsinki, Helsinki, Finland, Department of Physics, Tsinghua University, Beijing, China, Department of Signal Processing and Department of Information and Computer Science, Aalto University, Esbo, Finland Department of Communication Theory, KTH Royal Institute of Technology, Stockholm, Sweden, Department of Mathematics, Oregon State University, Corvallis, OR, USA, Systems Biology program, KTH Royal Institute of Technology, Sweden, Aalto University, Esbo, Finland, Department of Computational Biology, KTH Royal Institute of Technology, Stockholm, Sweden, Department of Mathematics and Statistics, University of Helsinki, Helsinki, Finland, Department of Physics, Tsinghua University, Beijing, China, Department of Signal Processing and Department of Information and Computer Science, Aalto University, Esbo, Finland.
authors.forename: Erik
authors.initials: E
authors.lastname: Aurell
authors.affiliation: Department of Communication Theory, KTH Royal Institute of Technology, Stockholm, Sweden, Department of Mathematics, Oregon State University, Corvallis, OR, USA, Systems Biology program, KTH Royal Institute of Technology, Sweden, Aalto University, Esbo, Finland, Department of Computational Biology, KTH Royal Institute of Technology, Stockholm, Sweden, Department of Mathematics and Statistics, University of Helsinki, Helsinki, Finland, Department of Physics, Tsinghua University, Beijing, China, Department of Signal Processing and Department of Information and Computer Science, Aalto University, Esbo, Finland.
authors.forename: Jukka
authors.initials: J
authors.lastname: Corander
mesh_terms: D000465:Algorithms; D001419:Bacteria / Q000145:classification* / Q000235:genetics; D059014:High-Throughput Nucleotide Sequencing; D056186:Metagenomics / Q000379:methods*; D015233:Models, Statistical; D012336:RNA, Ribosomal, 16S / Q000235:genetics; D017422:Sequence Analysis, DNA
chemical_list: D012336:RNA, Ribosomal, 16S