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

Abstract

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. As a result, this bioinformatics platform is an initial attempt at Empowering the Development of Genomics Expertise (EDGE) in a wide range of applications for microbial research.

Authors:
 [1];  [1];  [2];  [1];  [3];  [1];  [1];  [1];  [4]; ORCiD logo [1]
  1. Los Alamos National Lab. (LANL), Los Alamos, NM (United States)
  2. Defense Threat Reduction Agency, Fort Belvoir, VA (United States); Naval Medical Research Center-Frederick, Fort Detrick, MD (United States)
  3. Naval Medical Research Center-Frederick, Fort Detrick, MD (United States); Henry M. Jackson Foundation, Bethesda, MD (United States)
  4. Naval Medical Research Center-Frederick, Fort Detrick, MD (United States)
Publication Date:
Research Org.:
Los Alamos National Laboratory (LANL), Los Alamos, NM (United States)
Sponsoring Org.:
USDOD; USDOE
OSTI Identifier:
1342855
Report Number(s):
LA-UR-15-27035; LA-UR-15-22467
Journal ID: ISSN 0305-1048; TRN: US1701210
Grant/Contract Number:  
AC52-06NA25396
Resource Type:
Accepted Manuscript
Journal Name:
Nucleic Acids Research
Additional Journal Information:
Journal Volume: 45; Journal Issue: 1; Conference: DHS Biodetection strategy meeting, Los Alamos, NM (United States), 15-16 Apr 2015; Journal ID: ISSN 0305-1048
Publisher:
Oxford University Press
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; 97 MATHEMATICS AND COMPUTING; Biological Science; Computer Science; cloud compatible bioinformatics pipelines and workflows; integrated web-based genome analysis; isolate and metagenome NGS data analysis and visualization; next generation sequencing genomics and metagenome

Citation Formats

Li, Po-E, Lo, Chien -Chi, Anderson, Joseph J., Davenport, Karen W., Bishop-Lilly, Kimberly A., Xu, Yan, Ahmed, Sanaa, Feng, Shihai, Mokashi, Vishwesh P., and Chain, Patrick S. G. Enabling the democratization of the genomics revolution with a fully integrated web-based bioinformatics platform. United States: N. p., 2016. Web. doi:10.1093/nar/gkw1027.
Li, Po-E, Lo, Chien -Chi, Anderson, Joseph J., Davenport, Karen W., Bishop-Lilly, Kimberly A., Xu, Yan, Ahmed, Sanaa, Feng, Shihai, Mokashi, Vishwesh P., & Chain, Patrick S. G. Enabling the democratization of the genomics revolution with a fully integrated web-based bioinformatics platform. United States. https://doi.org/10.1093/nar/gkw1027
Li, Po-E, Lo, Chien -Chi, Anderson, Joseph J., Davenport, Karen W., Bishop-Lilly, Kimberly A., Xu, Yan, Ahmed, Sanaa, Feng, Shihai, Mokashi, Vishwesh P., and Chain, Patrick S. G. Thu . "Enabling the democratization of the genomics revolution with a fully integrated web-based bioinformatics platform". United States. https://doi.org/10.1093/nar/gkw1027. https://www.osti.gov/servlets/purl/1342855.
@article{osti_1342855,
title = {Enabling the democratization of the genomics revolution with a fully integrated web-based bioinformatics platform},
author = {Li, Po-E and Lo, Chien -Chi and Anderson, Joseph J. and Davenport, Karen W. and Bishop-Lilly, Kimberly A. and Xu, Yan and Ahmed, Sanaa and Feng, Shihai and Mokashi, Vishwesh P. and Chain, Patrick S. G.},
abstractNote = {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. As a result, this bioinformatics platform is an initial attempt at Empowering the Development of Genomics Expertise (EDGE) in a wide range of applications for microbial research.},
doi = {10.1093/nar/gkw1027},
journal = {Nucleic Acids Research},
number = 1,
volume = 45,
place = {United States},
year = {Thu Nov 24 00:00:00 EST 2016},
month = {Thu Nov 24 00:00:00 EST 2016}
}

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Cited by: 99 works
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Kraken: ultrafast metagenomic sequence classification using exact alignments
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Rapid evaluation and quality control of next generation sequencing data with FaQCs
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Supporting community annotation and user collaboration in the integrated microbial genomes (IMG) system
journal, April 2016


Reagent and laboratory contamination can critically impact sequence-based microbiome analyses
journal, November 2014


Next-generation sequencing diagnostics of bacteremia in septic patients
journal, July 2016


Automated ensemble assembly and validation of microbial genomes
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  • Koren, Sergey; Treangen, Todd J.; Hill, Christopher M.
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FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments
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Bacterial Pathogens in the Nasopharynx, Nasal Cavity, and Osteomeatal Complex during Wellness and Viral Infection
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Direct-from-blood RNA sequencing identifies the cause of post-bronchoscopy fever
journal, October 2019

  • Ko, Emily R.; Philipson, Casandra W.; Burke, Thomas W.
  • BMC Infectious Diseases, Vol. 19, Issue 1
  • DOI: 10.1186/s12879-019-4462-9

Complete genome sequences of Clostridium perfringens Del1 strain isolated from chickens affected by necrotic enteritis
journal, November 2017


Sunbeam: an extensible pipeline for analyzing metagenomic sequencing experiments
journal, March 2019


Effects of cadmium perturbation on the microbial community structure and heavy metal resistome of a tropical agricultural soil
journal, May 2020

  • Salam, Lateef B.; Obayori, Oluwafemi S.; Ilori, Mathew O.
  • Bioresources and Bioprocessing, Vol. 7, Issue 1
  • DOI: 10.1186/s40643-020-00314-w

Next-Generation Sequencing for Biodefense: Biothreat Detection, Forensics, and the Clinic
journal, March 2019


A Review of Bioinformatics Tools for Bio-Prospecting from Metagenomic Sequence Data
journal, March 2017

  • Roumpeka, Despoina D.; Wallace, R. John; Escalettes, Frank
  • Frontiers in Genetics, Vol. 8
  • DOI: 10.3389/fgene.2017.00023

Advances and Challenges in Metatranscriptomic Analysis
journal, September 2019


Offline Next Generation Metagenomics Sequence Analysis Using MinION Detection Software (MINDS)
journal, January 2019


Characterizing Phage Genomes for Therapeutic Applications
journal, April 2018

  • Philipson, Casandra; Voegtly, Logan; Lueder, Matthew
  • Viruses, Vol. 10, Issue 4
  • DOI: 10.3390/v10040188

Morphology and chemical behavior of model CsO x /Cu 2 O/Cu(111) nanocatalysts for methanol synthesis: Reaction with CO 2 and H 2
journal, January 2020

  • Hamlyn, Rebecca; Mahapatra, Mausumi; Orozco, Ivan
  • The Journal of Chemical Physics, Vol. 152, Issue 4
  • DOI: 10.1063/1.5129152

Microbial Diversity in Bushmeat Samples Recovered from the Serengeti Ecosystem in Tanzania
journal, December 2019


Standardized phylogenetic and molecular evolutionary analysis applied to species across the microbial tree of life
journal, February 2020


Systematic processing of ribosomal RNA gene amplicon sequencing data
journal, December 2019


Ten Genome Sequences of Human and Livestock Isolates of Bacillus anthracis from the Country of Georgia
journal, May 2017

  • Khmaladze, Ekaterine; Dzavashvili, Giorgi; Chanturia, Gvantsa
  • Genome Announcements, Vol. 5, Issue 19
  • DOI: 10.1128/genomea.00256-17

Complete Genome Sequence of a Parabacteroides distasonis Strain (CavFT hAR46) Isolated from a Gut Wall-Cavitating Microlesion in a Patient with Severe Crohn’s Disease
journal, September 2019

  • Yang, Falong; Kumar, Anand; Davenport, Karen Walston
  • Microbiology Resource Announcements, Vol. 8, Issue 36
  • DOI: 10.1128/mra.00585-19

Complete Genome Sequences of Historic Clostridioides difficile Food-Dwelling Ribotype 078 Strains in Canada Identical to That of the Historic Human Clinical Strain M120 in the United Kingdom
journal, September 2018

  • Kumar, Anand; Davenport, Karen Walston; Vuyisich, Grace
  • Microbiology Resource Announcements, Vol. 7, Issue 12
  • DOI: 10.1128/mra.00853-18

Draft Genome Sequence of the Industrially Significant Bacterium Pseudomonas fluorescens ATCC 13525
journal, November 2018

  • Meier, M. J.; Subasinghe, R. M.; Beaudette, L. A.
  • Microbiology Resource Announcements, Vol. 7, Issue 17
  • DOI: 10.1128/mra.01368-18

Draft Genome Sequence of the Industrially Significant Bacterium Bacillus amyloliquefaciens NRRL 942
journal, November 2018

  • Meier, Matthew J.; Dodge, Annette; Beaudette, Lee A.
  • Microbiology Resource Announcements, Vol. 7, Issue 18
  • DOI: 10.1128/mra.01374-18

High-Quality Draft Genome Sequence of Pseudomonas aeruginosa 268 Isolated from a Patient with a Left Ventricular Assist Device
journal, January 2019

  • Voegtly, Logan J.; Rice, Gregory K.; Cer, Regina Z.
  • Microbiology Resource Announcements, Vol. 8, Issue 1
  • DOI: 10.1128/mra.01403-18

Complete genome sequences of Clostridium perfringens Del1 strain isolated from chickens affected by necrotic enteritis
journal, November 2017


Sunbeam: an extensible pipeline for analyzing metagenomic sequencing experiments
journal, March 2019


Multiplex PCR−Based Next-Generation Sequencing and Global Diversity of Seoul Virus in Humans and Rats
journal, February 2018

  • Kim, Won-Keun; No, Jin Sun; Lee, Seung-Ho
  • Emerging Infectious Diseases, Vol. 24, Issue 2
  • DOI: 10.3201/eid2402.171216

Advances and Challenges in Metatranscriptomic Analysis
journal, September 2019


An Integrated Pipeline for Annotation and Visualization of Metagenomic Contigs
journal, October 2019


Constructing and Characterizing Bacteriophage Libraries for Phage Therapy of Human Infections
journal, November 2019

  • Gibson, Shelley B.; Green, Sabrina I.; Liu, Carmen Gu
  • Frontiers in Microbiology, Vol. 10
  • DOI: 10.3389/fmicb.2019.02537

Offline Next Generation Metagenomics Sequence Analysis Using MinION Detection Software (MINDS)
journal, January 2019


Characterization of Unknown Orthobunya-Like Viruses from India
journal, August 2018

  • Whitmer, Shannon; Yadav, Pragya; Sarkale, Prasad
  • Viruses, Vol. 10, Issue 9
  • DOI: 10.3390/v10090451