MT-Toolbox: improved amplicon sequencing using molecule tags

Public Deposited
Analytics

Downloadable Content

Download PDF
Request Version for Screen Reader
Creator
  • Yourstone, Scott M
    • Affiliation: School of Medicine, Curriculum in Bioinformatics and Computational Biology
  • Lundberg, Derek S
    • Affiliation: College of Arts and Sciences, Department of Biology
  • Dangl, Jeffery L.
    • Affiliation: School of Medicine, Department of Microbiology and Immunology
    • Other Affiliation: Howard Hughes Medical Institute, University of North Carolina
  • Jones, Corbin
    • Affiliation: College of Arts and Sciences, Department of Biology
Abstract
  • Background Short oligonucleotides can be used as markers to tag and track DNA sequences. For example, barcoding techniques (i.e. Multiplex Identifiers or Indexing) use short oligonucleotides to distinguish between reads from different DNA samples pooled for high-throughput sequencing. A similar technique called molecule tagging uses the same principles but is applied to individual DNA template molecules. Each template molecule is tagged with a unique oligonucleotide prior to polymerase chain reaction. The resulting amplicon sequences can be traced back to their original templates by their oligonucleotide tag. Consensus building from sequences sharing the same tag enables inference of original template molecules thereby reducing effects of sequencing error and polymerase chain reaction bias. Several independent groups have developed similar protocols for molecule tagging; however, user-friendly software for build consensus sequences from molecule tagged reads is not readily available or is highly specific for a particular protocol. Results MT-Toolbox recognizes oligonucleotide tags in amplicons and infers the correct template sequence. On a set of molecule tagged test reads, MT-Toolbox generates sequences having on average 0.00047 errors per base. MT-Toolbox includes a graphical user interface, command line interface, and options for speed and accuracy maximization. It can be run in serial on a standard personal computer or in parallel on a Load Sharing Facility based cluster system. An optional plugin provides features for common 16S metagenome profiling analysis such as chimera filtering, building operational taxonomic units, contaminant removal, and taxonomy assignments. Conclusions MT-Toolbox provides an accessible, user-friendly environment for analysis of molecule tagged reads thereby reducing technical errors and polymerase chain reaction bias. These improvements reduce noise and allow for greater precision in single amplicon sequencing experiments.
Date of publication
DOI
Identifier
Resource type
  • Article
Rights statement
  • In Copyright
Rights holder
  • Scott M Yourstone et al.; licensee BioMed Central Ltd.
License
Journal title
  • BMC Bioinformatics
Journal volume
  • 15
Journal issue
  • 1
Page start
  • 284
Language
  • English
Is the article or chapter peer-reviewed?
  • Yes
ISSN
  • 1471-2105
Bibliographic citation
  • BMC Bioinformatics. 2014 Aug 22;15(1):284
Publisher
  • BioMed Central Ltd
Access right
  • Open Access
Date uploaded
  • August 26, 2015

Relations

Parents:

This work has no parents.

Items

Thumbnail Title Date Uploaded Visibility Actions
file details 1471-2105-15-284.pdf 2019-05-07 Public Download
file details Source code for MT-MT-Toolbox-v4.1.0. 2019-05-07 Public Download
file details Supplementary Information. Note S.1. 2019-05-07 Public Download
file details Source code for BioUtils-v1.0.9. 2019-05-07 Public Download
file details Source code for MT-Toolbox-v4.1.0 2019-05-07 Public Download