IM-TORNADO: A tool for comparison of 16S reads from paired-end libraries

Patricio Jeraldo, Krishna R Kalari, Xianfeng Chen, Jaysheel Bhavsar, Ashutosh Mangalam, Bryan White, Heidi Nelson, Jean-Pierre Kocher, Nicholas D Chia

Research output: Contribution to journalArticle

49 Scopus citations

Abstract

Motivation: 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. Availability and Implementation: 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.

Original languageEnglish (US)
Article numbere114804
JournalPLoS One
Volume9
Issue number12
DOIs
StatePublished - Dec 15 2014

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ASJC Scopus subject areas

  • Agricultural and Biological Sciences(all)
  • Biochemistry, Genetics and Molecular Biology(all)
  • Medicine(all)

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