title: IM-TORNADO: a tool for comparison of 16S reads from paired-end libraries.
abstract: BACKGROUND
  16S rDNA hypervariable tag sequencing has become the de facto method for accessing microbial diversity. Illumina paired-end sequencing, which produces two separate reads for each DNA fragment, has become the platform of choice for this application. However, when the two reads do not overlap, existing computational pipelines analyze data from read separately and underutilize the information contained in the paired-end reads.
  
  
  RESULTS
  We created a workflow known as Illinois Mayo Taxon Organization from RNA Dataset Operations (IM-TORNADO) for processing non-overlapping reads while retaining maximal information content. Using synthetic mock datasets, we show that the use of both reads produced answers with greater correlation to those from full length 16S rDNA when looking at taxonomy, phylogeny, and beta-diversity.
  
  
  METHODS
  IM-TORNADO is freely available at http://sourceforge.net/projects/imtornado and produces BIOM format output for cross compatibility with other pipelines such as QIIME, mothur, and phyloseq.
authors.affiliation: Department of Surgery, Mayo Clinic, Rochester, Minnesota, United States of America; Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America.
authors.forename: Patricio
authors.initials: P
authors.lastname: Jeraldo
authors.affiliation: Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota, United States of America.
authors.forename: Krishna
authors.initials: K
authors.lastname: Kalari
authors.affiliation: Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota, United States of America.
authors.forename: Xianfeng
authors.initials: X
authors.lastname: Chen
authors.affiliation: Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota, United States of America.
authors.forename: Jaysheel
authors.initials: J
authors.lastname: Bhavsar
authors.affiliation: Department of Immunology, Mayo Clinic, Rochester, Minnesota, United States of America.
authors.forename: Ashutosh
authors.initials: A
authors.lastname: Mangalam
authors.affiliation: Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America; Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America.
authors.forename: Bryan
authors.initials: B
authors.lastname: White
authors.affiliation: Department of Surgery, Mayo Clinic, Rochester, Minnesota, United States of America.
authors.forename: Heidi
authors.initials: H
authors.lastname: Nelson
authors.affiliation: Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota, United States of America.
authors.forename: Jean-Pierre
authors.initials: JP
authors.lastname: Kocher
authors.affiliation: Department of Surgery, Mayo Clinic, Rochester, Minnesota, United States of America; Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America; Department of Physiology and Biomedical Engineering, Mayo Clinic College of Medicine, Rochester, Minnesota, United States of America.
authors.forename: Nicholas
authors.initials: N
authors.lastname: Chia
mesh_terms: D015723:Gene Library; D020459:Genes, rRNA; D006801:Humans; D064307:Microbiota; D010802:Phylogeny; D012336:RNA, Ribosomal, 16S / Q000235:genetics*; D017422:Sequence Analysis, DNA / Q000379:methods; D012984:Software
chemical_list: D012336:RNA, Ribosomal, 16S