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PLoS One. 2014 Dec 15;9(12):e114804. doi: 10.1371/journal.pone.0114804. eCollection 2014.

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

Author information

1
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.
2
Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota, United States of America.
3
Department of Immunology, Mayo Clinic, Rochester, Minnesota, United States of America.
4
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.
5
Department of Surgery, Mayo Clinic, Rochester, Minnesota, United States of America.
6
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.

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.

PMID:
25506826
PMCID:
PMC4266640
DOI:
10.1371/journal.pone.0114804
[Indexed for MEDLINE]
Free PMC Article

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