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

46 Citations (Scopus)

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

Fingerprint

Ribosomal DNA
Libraries
Pipelines
RNA
Taxonomies
Workflow
Availability
Phylogeny
taxonomy
DNA
phylogeny
Processing
Datasets
methodology

ASJC Scopus subject areas

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

Cite this

IM-TORNADO : A tool for comparison of 16S reads from paired-end libraries. / Jeraldo, Patricio; Kalari, Krishna R; Chen, Xianfeng; Bhavsar, Jaysheel; Mangalam, Ashutosh; White, Bryan; Nelson, Heidi; Kocher, Jean-Pierre; Chia, Nicholas D.

In: PLoS One, Vol. 9, No. 12, e114804, 15.12.2014.

Research output: Contribution to journalArticle

Jeraldo, Patricio ; Kalari, Krishna R ; Chen, Xianfeng ; Bhavsar, Jaysheel ; Mangalam, Ashutosh ; White, Bryan ; Nelson, Heidi ; Kocher, Jean-Pierre ; Chia, Nicholas D. / IM-TORNADO : A tool for comparison of 16S reads from paired-end libraries. In: PLoS One. 2014 ; Vol. 9, No. 12.
@article{5552897d1b9944ef8dca4ed5e07e8c15,
title = "IM-TORNADO: A tool for comparison of 16S reads from paired-end libraries",
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.",
author = "Patricio Jeraldo and Kalari, {Krishna R} and Xianfeng Chen and Jaysheel Bhavsar and Ashutosh Mangalam and Bryan White and Heidi Nelson and Jean-Pierre Kocher and Chia, {Nicholas D}",
year = "2014",
month = "12",
day = "15",
doi = "10.1371/journal.pone.0114804",
language = "English (US)",
volume = "9",
journal = "PLoS One",
issn = "1932-6203",
publisher = "Public Library of Science",
number = "12",

}

TY - JOUR

T1 - IM-TORNADO

T2 - A tool for comparison of 16S reads from paired-end libraries

AU - Jeraldo, Patricio

AU - Kalari, Krishna R

AU - Chen, Xianfeng

AU - Bhavsar, Jaysheel

AU - Mangalam, Ashutosh

AU - White, Bryan

AU - Nelson, Heidi

AU - Kocher, Jean-Pierre

AU - Chia, Nicholas D

PY - 2014/12/15

Y1 - 2014/12/15

N2 - 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.

AB - 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.

UR - http://www.scopus.com/inward/record.url?scp=84918559643&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=84918559643&partnerID=8YFLogxK

U2 - 10.1371/journal.pone.0114804

DO - 10.1371/journal.pone.0114804

M3 - Article

C2 - 25506826

AN - SCOPUS:84918559643

VL - 9

JO - PLoS One

JF - PLoS One

SN - 1932-6203

IS - 12

M1 - e114804

ER -