title: PhyloToAST: Bioinformatics tools for species-level analysis and visualization of complex microbial datasets.
abstract: The 16S rRNA gene is widely used for taxonomic profiling of microbial ecosystems; and recent advances in sequencing chemistry have allowed extremely large numbers of sequences to be generated from minimal amounts of biological samples. Analysis speed and resolution of data to species-level taxa are two important factors in large-scale explorations of complex microbiomes using 16S sequencing. We present here new software, Phylogenetic Tools for Analysis of Species-level Taxa (PhyloToAST), that completely integrates with the QIIME pipeline to improve analysis speed, reduce primer bias (requiring two sequencing primers), enhance species-level analysis, and add new visualization tools. The code is free and open source, and can be accessed at http://phylotoast.org.
authors.affiliation: Division of Periodontology, College of Dentistry, The Ohio State University, Columbus, Ohio, USA.
authors.forename: Shareef M
authors.initials: SM
authors.lastname: Dabdoub
authors.affiliation: Division of Periodontology, College of Dentistry, The Ohio State University, Columbus, Ohio, USA.
authors.forename: Megan L
authors.initials: ML
authors.lastname: Fellows
authors.affiliation: Division of Periodontology, College of Dentistry, The Ohio State University, Columbus, Ohio, USA.
authors.forename: Akshay D
authors.initials: AD
authors.lastname: Paropkari
authors.affiliation: Division of Biosciences, College of Dentistry, The Ohio State University, Columbus, Ohio, USA.
authors.forename: Matthew R
authors.initials: MR
authors.lastname: Mason
authors.affiliation: Division of Orthodontics, College of Dentistry, University of Kentucky, Lexington, Kentucky, USA.
authors.forename: Sarandeep S
authors.initials: SS
authors.lastname: Huja
authors.affiliation: Division of Periodontics, Eastman Institute for Oral Health, School of Medicine and Dentistry, University of Rochester, Rochester, NY, USA.
authors.forename: Alexandra A
authors.initials: AA
authors.lastname: Tsigarida
authors.affiliation: Division of Periodontology, College of Dentistry, The Ohio State University, Columbus, Ohio, USA.
authors.forename: Purnima S
authors.initials: PS
authors.lastname: Kumar
mesh_terms: D001419:Bacteria / Q000145:classification / Q000235:genetics*; D044822:Biodiversity; D019295:Computational Biology; D059014:High-Throughput Nucleotide Sequencing; D064307:Microbiota / Q000235:genetics*; D010802:Phylogeny; D012336:RNA, Ribosomal, 16S / Q000235:genetics; D012984:Software
chemical_list: D012336:RNA, Ribosomal, 16S