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

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

doi:10.1371/journal.pone.0114804

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

Journal article

Open access

Peer reviewed

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

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

PloS one, Vol.9(12), e114804

2014

DOI: 10.1371/journal.pone.0114804

PMCID: PMC4266640

PMID: 25506826

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Abstract

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. 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. 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.

Software

Microbiota

Gene Library

Humans

RNA, Ribosomal, 16S - genetics

Genes, rRNA

Phylogeny

Sequence Analysis, DNA - methods

Details

Title: Subtitle: IM-TORNADO: a tool for comparison of 16S reads from paired-end libraries
Creators: Patricio Jeraldo - 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
Krishna Kalari - Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota, United States of America
Xianfeng Chen - Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota, United States of America
Jaysheel Bhavsar - Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota, United States of America
Ashutosh Mangalam - Department of Immunology, Mayo Clinic, Rochester, Minnesota, United States of America
Bryan White - University of Illinois Urbana-Champaign
Heidi Nelson - Department of Surgery, Mayo Clinic, Rochester, Minnesota, United States of America
Jean-Pierre Kocher - Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota, United States of America
Nicholas Chia - Mayo Clinic
Resource Type: Journal article
Publication Details: PloS one, Vol.9(12), e114804
DOI: 10.1371/journal.pone.0114804
PMID: 25506826
PMCID: PMC4266640
NLM abbreviation: PLoS One
ISSN: 1932-6203
eISSN: 1932-6203
Publisher: United States
Grant note: R01 CA179243 / NCI NIH HHS
Language: English
Date published: 2014
Academic Unit: Pathology; Iowa Neuroscience Institute
Record Identifier: 9983905530202771

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