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dc.contributor.author Jeraldo, Patricio
dc.contributor.author Kalari, Krishna
dc.contributor.author Chen, Xianfeng
dc.contributor.author Bhavsar, Jaysheel
dc.contributor.author Mangalam, Ashutosh
dc.contributor.author White, Bryan
dc.contributor.author Nelson, Heidi
dc.contributor.author Kocher, Jean-Pierre
dc.contributor.author Chia, Nicholas
dc.date.accessioned 2014-12-30T21:17:49Z
dc.date.available 2014-12-30T21:17:49Z
dc.date.issued 2014-12-15
dc.identifier doi:10.5061/dryad.fm67n
dc.identifier.citation Jeraldo P, Kalari K, Chen X, Bhavsar J, Mangalam A, White B, Nelson H, Kocher J, Chia N (2014) IM-TORNADO: a tool for comparison of 16S reads from paired-end libraries. PLoS ONE 9(12): e114804.
dc.identifier.uri http://hdl.handle.net/10255/dryad.73732
dc.description 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/imtornad​o and produces BIOM format output for cross compatibility with other pipelines such as QIIME, mothur, and phyloseq.
dc.relation.haspart doi:10.5061/dryad.fm67n/1
dc.relation.haspart doi:10.5061/dryad.fm67n/2
dc.relation.haspart doi:10.5061/dryad.fm67n/3
dc.relation.haspart doi:10.5061/dryad.fm67n/4
dc.relation.haspart doi:10.5061/dryad.fm67n/5
dc.relation.haspart doi:10.5061/dryad.fm67n/6
dc.relation.isreferencedby doi:10.1371/journal.pone.0114804
dc.relation.isreferencedby PMID:25506826
dc.subject microbiome
dc.subject 16S rDNA
dc.subject paired-end sequencing
dc.subject bioinformatics
dc.title Data from: IM-TORNADO: a tool for comparison of 16S reads from paired-end libraries
dc.type Article
dwc.ScientificName Bacteria
dwc.ScientificName Archaea
prism.publicationName PLOS ONE

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Title Files for taxonomy comparison
Downloaded 1491 times
Description Synthetic mock dataset used for taxonomy assignment comparison, across multiple read lengths. File includes scripts used and raw validation data.
Download comparison_taxonomy.tar.bz2 (203.9 Mb)
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Title Files for comparison of sequence aligners
Downloaded 2359 times
Description Synthetic mock datasets used to compare the mulitple sequence aligners cmalign (from the infernal package) versus the NAST algorithm (from the PyNAST implementation). File includes R scripts and resulting raw validation data.
Download comparison_aligners.tar.bz2 (222.0 Mb)
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Title Files for validation with realistic synthetic reads
Downloaded 11520 times
Description Synthetic mock datasets used for validation based on a realistic human stool microbiome dataset. These are NOT real bacterial reads. Those reads are available as example data from the IM-TORNADO pipeline. File includes scripts and raw validation data.
Download validation_realistic.tar.bz2 (440.2 Mb)
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Title Files for taxonomy comparison using reads with errors
Downloaded 38 times
Description Synthetic mock datasets (100 replicates) used for validation of taxonomy using reads with errors and different length. File also includes scripts and resulting raw data for the validation.
Download validation_taxonomy_errors.tar.bz2 (6.451 Gb)
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Title Files for validation of beta diversity using 16S rDNA regions V3 to V5
Downloaded 13450 times
Description Synthetic mock datasets (100 replicates) used for validation of beta diversity across synthetic communities using 16S rDNA region V3 to V5. File also includes scripts and resulting raw data for the validation.
Download validation_V3V5.tar.bz2 (3.864 Gb)
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Title Files for validation of beta diversity using 16S rDNA regions V6 to V9
Downloaded 22229 times
Description Synthetic mock datasets (100 replicates) used for validation of beta diversity across synthetic communities using 16S rDNA region V6 to V9. File also includes scripts and resulting raw data for the validation.
Download validation_V6V9.tar.bz2 (3.403 Gb)
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