Enabling the democratization of the genomics revolution with a fully integrated web-based bioinformatics platform

Continued advancements in sequencing technologies have fueled the development of new sequencing applications and promise to flood current databases with raw data. A number of factors prevent the seamless and easy use of these data, including the breadth of project goals, the wide array of tools that individually perform fractions of any given analysis, the large number of associated software/hardware dependencies, and the detailed expertise required to perform these analyses. To address these issues, we have developed an intuitive web-based environment with a wide assortment of integrated and cutting-edge bioinformatics tools in pre-configured workflows. These workflows, coupled with the ease of use of the environment, provide even novice next-generation sequencing users with the ability to perform many complex analyses with only a few mouse clicks and, within the context of the same environment, to visualize and further interrogate their results. This bioinformatics platform is an initial attempt at Empowering the Development of Genomics Expertise (EDGE) in a wide range of applications for microbial research.

[1]  L. Stein,et al.  JBrowse: a next-generation genome browser. , 2009, Genome research.

[2]  Sergey Koren,et al.  Automated ensemble assembly and validation of microbial genomes , 2014, BMC Bioinformatics.

[3]  S. Losito,et al.  PCR Assay To Detect Bacillus anthracis Spores in Heat-Treated Specimens , 2003, Journal of Clinical Microbiology.

[4]  Siu-Ming Yiu,et al.  IDBA-UD: a de novo assembler for single-cell and metagenomic sequencing data with highly uneven depth , 2012, Bioinform..

[5]  N. Blom,et al.  The microbiome of New World vultures , 2014, Nature Communications.

[6]  R. Daber,et al.  Understanding the limitations of next generation sequencing informatics, an approach to clinical pipeline validation using artificial data sets. , 2013, Cancer genetics.

[7]  E. Koonin,et al.  Novel Bacteriophages Containing a Genome of Another Bacteriophage within Their Genomes , 2012, PloS one.

[8]  Sergey I. Nikolenko,et al.  SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing , 2012, J. Comput. Biol..

[9]  A. C. Munk,et al.  Thirty-Two Complete Genome Assemblies of Nine Yersinia Species, Including Y. pestis, Y. pseudotuberculosis, and Y. enterocolitica , 2015, Genome Announcements.

[10]  Natalia N. Ivanova,et al.  Supporting community annotation and user collaboration in the integrated microbial genomes (IMG) system , 2016, BMC Genomics.

[11]  Jeffrey L. Curtis,et al.  Analysis of the Upper Respiratory Tract Microbiotas as the Source of the Lung and Gastric Microbiotas in Healthy Individuals , 2015, mBio.

[12]  E. D. Hyman.  A new method of sequencing DNA. , 1988, Analytical biochemistry.

[13]  Z. Iqbal,et al.  Rapid Whole-Genome Sequencing for Surveillance of Salmonella enterica Serovar Enteritidis , 2014, Emerging infectious diseases.

[14]  Martin Kircher,et al.  Double indexing overcomes inaccuracies in multiplex sequencing on the Illumina platform , 2011, Nucleic acids research.

[15]  J. Mesirov,et al.  GenePattern 2.0 , 2006, Nature Genetics.

[16]  Po-E Li,et al.  Accurate read-based metagenome characterization using a hierarchical suite of unique signatures , 2015, Nucleic acids research.

[17]  Gonçalo R. Abecasis,et al.  The Sequence Alignment/Map format and SAMtools , 2009, Bioinform..

[18]  F. Schaefer,et al.  Performance of Traditional and Molecular Methods for Detecting Biological Agents in Drinking Water , 2009 .

[19]  F. Sanger,et al.  DNA sequencing with chain-terminating inhibitors. , 1977, Proceedings of the National Academy of Sciences of the United States of America.

[20]  J. Côté,et al.  Bacillus weihenstephanensis characteristics are present in Bacillus cereus and Bacillus mycoides strains. , 2013, FEMS microbiology letters.

[21]  Robert C. Thompson,et al.  Genome-wide association and meta-analysis of bipolar disorder in individuals of European ancestry , 2009, Proceedings of the National Academy of Sciences.

[22]  T. Schwan,et al.  New method for plague surveillance using polymerase chain reaction to detect Yersinia pestis in fleas , 1993, Journal of clinical microbiology.

[23]  S. Salzberg,et al.  Versatile and open software for comparing large genomes , 2004, Genome Biology.

[24]  Mihai Pop,et al.  Genomic characterization of the Yersinia genus , 2010, Genome Biology.

[25]  I-Min A. Chen,et al.  IMG/M 4 version of the integrated metagenome comparative analysis system , 2013, Nucleic Acids Res..

[26]  Yan Zhang,et al.  PATRIC, the bacterial bioinformatics database and analysis resource , 2013, Nucleic Acids Res..

[27]  Paramvir S. Dehal,et al.  FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments , 2010, PloS one.

[28]  Po-E Li,et al.  From raw reads to trees: Whole genome SNP phylogenetics across the tree of life , 2015, bioRxiv.

[29]  Jonas Korlach,et al.  Single-molecule sequencing to track plasmid diversity of hospital-associated carbapenemase-producing Enterobacteriaceae , 2014, Science Translational Medicine.

[30]  G. Asiki,et al.  Pneumonic Plague Cluster, Uganda, 2004 , 2006, Emerging infectious diseases.

[31]  E. Myers,et al.  Basic local alignment search tool. , 1990, Journal of molecular biology.

[32]  Adam M. Phillippy,et al.  Interactive metagenomic visualization in a Web browser , 2011, BMC Bioinformatics.

[33]  Derrick E. Wood,et al.  Kraken: ultrafast metagenomic sequence classification using exact alignments , 2014, Genome Biology.

[34]  Fangfang Xia,et al.  The SEED and the Rapid Annotation of microbial genomes using Subsystems Technology (RAST) , 2013, Nucleic Acids Res..

[35]  Thomas D. Otto,et al.  RATT: Rapid Annotation Transfer Tool , 2011, Nucleic acids research.

[36]  M. Biebl,et al.  Ralstonia pickettii-innocent bystander or a potential threat? , 2006, Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases.

[37]  B. Faircloth,et al.  Primer3—new capabilities and interfaces , 2012, Nucleic acids research.

[38]  Joseph K. Han,et al.  Bacterial pathogens in the nasopharynx, nasal cavity, and osteomeatal complex during wellness and viral infection , 2013, American Journal of Rhinology & Allergy.

[39]  Chien-Chi Lo,et al.  Rapid evaluation and quality control of next generation sequencing data with FaQCs , 2014, BMC Bioinformatics.

[40]  Steven L Salzberg,et al.  Fast gapped-read alignment with Bowtie 2 , 2012, Nature Methods.

[41]  C. Huttenhower,et al.  Metagenomic microbial community profiling using unique clade-specific marker genes , 2012, Nature Methods.

[42]  James R. Knight,et al.  Genome sequencing in microfabricated high-density picolitre reactors , 2005, Nature.

[43]  Anna Lipzen,et al.  Comparative Genomics of Saccharomyces cerevisiae Natural Isolates for Bioenergy Production , 2014, Genome biology and evolution.

[44]  Alexandros Stamatakis,et al.  RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies , 2014, Bioinform..

[45]  J. T. Dunnen,et al.  Next generation sequencing technology: Advances and applications. , 2014, Biochimica et biophysica acta.

[46]  Xiaoxu Tian,et al.  RNA-seq based identification and mutant validation of gene targets related to ethanol resistance in cyanobacterial Synechocystis sp. PCC 6803 , 2012, Biotechnology for Biofuels.

[47]  S. Bennett.  Solexa Ltd. , 2004, Pharmacogenomics.

[48]  Samuel A. Smits,et al.  jsPhyloSVG: A Javascript Library for Visualizing Interactive and Vector-Based Phylogenetic Trees on the Web , 2010, PloS one.

[49]  Marc S. Williams,et al.  Pharmacogenomics , 2019, The Lancet.

[50]  Richard Durbin,et al.  Fast and accurate long-read alignment with Burrows–Wheeler transform , 2010, Bioinform..

[51]  Katherine H. Huang,et al.  A framework for human microbiome research , 2012, Nature.

[52]  Paul Turner,et al.  Reagent and laboratory contamination can critically impact sequence-based microbiome analyses , 2014, BMC Biology.

[53]  A. von Haeseler,et al.  Next-generation sequencing diagnostics of bacteremia in septic patients , 2016, Genome Medicine.

[54]  Daniel J. Blankenberg,et al.  Galaxy: A Web‐Based Genome Analysis Tool for Experimentalists , 2010, Current protocols in molecular biology.

[55]  D. Fouts.  Phage_Finder: Automated identification and classification of prophage regions in complete bacterial genome sequences , 2006, Nucleic acids research.

[56]  Torsten Seemann,et al.  Prokka: rapid prokaryotic genome annotation , 2014, Bioinform..

[57]  Maria Victoria Schneider,et al.  Next-generation sequencing: a challenge to meet the increasing demand for training workshops in Australia , 2013, Briefings Bioinform..

[58]  Elizabeth M Glass,et al.  MG-RAST, a Metagenomics Service for Analysis of Microbial Community Structure and Function. , 2016, Methods in molecular biology.