IM-TORNADO protocols

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IM-TORNADO specifications

Information


Unique identifier OMICS_12805
Name IM-TORNADO
Alternative name Illinois Mayo Taxon Organization from RNA Dataset Operations
Software type Pipeline/Workflow
Interface Command line interface
Restrictions to use None
Output data biom, tree, taxonomy, fasta, txt
Operating system Unix/Linux
Programming languages Python
License GNU General Public License version 3.0
Computer skills Advanced
Version 2.0.3.3
Stability Stable
Requirements
USEARCH, mothur, FastTree, genometools, Infernal, Trimmomatic, Java, perl, sed, awk genometools, VSEARCH, BioPython, BIOM-format, bitarray
Source code URL https://codeload.github.com/pjeraldo/imtornado2/zip/master
Maintained Yes

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Maintainer


  • person_outline Nicholas Chia <>

Publication for Illinois Mayo Taxon Organization from RNA Dataset Operations

IM-TORNADO in pipelines

 (2)
2017
PMCID: 5708741
PMID: 29190829
DOI: 10.1371/journal.pone.0188873

[…] and 3’ reads with average sliding window (size = 4) score of q15, using trimmomatic v 0.22 []. paired reads with that were at least 80% of the original read length nucleotides were aligned with the im-tornado 16s analysis pipeline[, ] using the greengenes taxonomy (greengenes99 database version 12.10) []. additional details are provided in ., to account for dispersion and sparsity, microbial […]

2016
PMCID: 5123330
PMID: 27884207
DOI: 10.1186/s13073-016-0368-y

[…] miseq (san diego, ca, usa) sequencing platform., sequence reads were aligned with our own custom multiple alignment tool known as the illinois-mayo taxon operations for rna dataset organization (im-tornado) that merges paired end reads into a single multiple alignment and obtains taxa calls []. im-tornado then clusters sequences into operational taxonomic units (otus) using abundantotu+ []., […]


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IM-TORNADO in publications

 (11)
PMCID: 5708741
PMID: 29190829
DOI: 10.1371/journal.pone.0188873

[…] and 3’ reads with average sliding window (size = 4) score of q15, using trimmomatic v 0.22 []. paired reads with that were at least 80% of the original read length nucleotides were aligned with the im-tornado 16s analysis pipeline[, ] using the greengenes taxonomy (greengenes99 database version 12.10) []. additional details are provided in ., to account for dispersion and sparsity, microbial […]

PMCID: 5353589
PMID: 28300212
DOI: 10.1038/srep44565

[…] end. cluster density was 964 k/mm2 with 85.9% of clusters passing filter., de-multiplexed forward (read 1) and reverse reads (read 2) obtained from the sequencing facility were processed using the im-tornado v2.0.3.2 pipeline. trimmomatic program was used to trim the forward and the reverse primers from the 5′ end of read 1 and read 2 respectively, and the adaptor sequences from the 3′ end […]

PMCID: 5345876
PMID: 28245239
DOI: 10.1371/journal.pntd.0005377

[…] miseq v3 bulk system. the libraries were sequenced from both ends of the molecules to a total read length of 300nt from each end. cluster density was 964k/mm2 with 85.9% of clusters passing filter., im-tornado 2.0.3.2 platform was used to process the de-multiplexed fasq-formatted files obtained from the sequencing facility. this platform is designed to process non-overlapping reads for analysis […]

PMCID: 5048651
PMID: 27716401
DOI: 10.1186/s13073-016-0357-1

[…] read2 (agtcagtcagccccgtcaattcmtttragt), and index (actyaaakgaattgacggggctgactgact) sequencing primers []. this produced non-overlapping reads, which were then analyzed by the im-tornado and mothur pipeline using default parameters [, ] (see details in additional file )., we summarized microbiota data using both alpha diversity and beta diversity. alpha diversity reflects […]

PMCID: 5028048
PMID: 27643883
DOI: 10.1371/journal.pone.0162803

[…] miseq platform and the miseq reagent kit v2 (2 x 250 reads, 500 cycles; illumina, inc.; san diego, ca). from this data, taxonomy was assigned and phylogenetic trees were constructed using the illinois mayo taxon organization from rna dataset operations (im-tornado) pipeline []., alpha diversity was calculated using four different measures using the “phyloseq” package in r []. the observed […]


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IM-TORNADO institution(s)
Department of Surgery, Mayo Clinic, Chinahester, MN, USA; Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA; Department of Health Sciences Research, Mayo Clinic, Chinahester, MN, USA; Department of Immunology, Mayo Clinic, Chinahester, MN, USA; Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, USA; Department of Physiology and Biomedical Engineering, Mayo Clinic College of Medicine, Chinahester, MN, USA
IM-TORNADO funding source(s)
This work was supported by the Mayo Clinic Center for Individualized Medicine Microbiome Program and by the MayoIllinois Strategic Alliance for Technology-Based Healthcare.

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