For Publishers
DiscoveryMetadataPeer reviewHostingPublishing
For Researchers
JoinPublishReviewCollect
Register
Blog
About
Search
Advanced search
My ScienceOpen
Search
For Publishers
For Researchers
Blog
About
4
views
14
references
 Top references
cited by
4
    
0 reviews
 Review
0
comments
 Comment
0
recommends
+1 Recommend
0 collections
    0
    shares
      298
      similar
       All similar
      • Record: found
      • Abstract: found
      • Article: found
      Is Open Access

      Complete Genome Sequence of Burkholderia cenocepacia K56-2, an Opportunistic Pathogen

      brief-report

      Read this article at

      ScienceOpenPublisherPMC
      Bookmark
          There is no author summary for this article yet. Authors can add summaries to their articles on ScienceOpen to make them more accessible to a non-specialist audience.

          Abstract

          Burkholderia cenocepacia K56-2, an opportunistic bacterium for people with cystic fibrosis (CF), belongs to the Burkholderia cepacia complex (Bcc) and is consistently used as a model pathogen. We describe here the closed genome sequence for this strain, which will help advance research in B. cenocepacia biology and omics studies.

          ABSTRACT

          Burkholderia cenocepacia K56-2, an opportunistic bacterium for people with cystic fibrosis (CF), belongs to the Burkholderia cepacia complex (Bcc) and is consistently used as a model pathogen. We describe here the closed genome sequence for this strain, which will help advance research in B. cenocepacia biology and omics studies.

          Related collections

          Most cited references14

          • Record: found
          • Abstract: found
          • Article: found
          Is Open Access

          Trimmomatic: a flexible trimmer for Illumina sequence data

          Anthony M. Bolger, Marc Lohse, Bjoern Usadel (2014)
          Motivation: Although many next-generation sequencing (NGS) read preprocessing tools already existed, we could not find any tool or combination of tools that met our requirements in terms of flexibility, correct handling of paired-end data and high performance. We have developed Trimmomatic as a more flexible and efficient preprocessing tool, which could correctly handle paired-end data. Results: The value of NGS read preprocessing is demonstrated for both reference-based and reference-free tasks. Trimmomatic is shown to produce output that is at least competitive with, and in many cases superior to, that produced by other tools, in all scenarios tested. Availability and implementation: Trimmomatic is licensed under GPL V3. It is cross-platform (Java 1.5+ required) and available at http://www.usadellab.org/cms/index.php?page=trimmomatic Contact: usadel@bio1.rwth-aachen.de Supplementary information: Supplementary data are available at Bioinformatics online.
          Article 0 comments Cited 16438 times – based on 0 reviews     Review now
            Bookmark
            • Record: found
            • Abstract: found
            • Article: not found

            Prokka: rapid prokaryotic genome annotation.

            T Seemann (2014)
            The multiplex capability and high yield of current day DNA-sequencing instruments has made bacterial whole genome sequencing a routine affair. The subsequent de novo assembly of reads into contigs has been well addressed. The final step of annotating all relevant genomic features on those contigs can be achieved slowly using existing web- and email-based systems, but these are not applicable for sensitive data or integrating into computational pipelines. Here we introduce Prokka, a command line software tool to fully annotate a draft bacterial genome in about 10 min on a typical desktop computer. It produces standards-compliant output files for further analysis or viewing in genome browsers. Prokka is implemented in Perl and is freely available under an open source GPLv2 license from http://vicbioinformatics.com/. © The Author 2014. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.
            Article 0 comments Cited 4662 times – based on 0 reviews     Review now
              Bookmark
              • Record: found
              • Abstract: found
              • Article: found
              Is Open Access

              Unicycler: Resolving bacterial genome assemblies from short and long sequencing reads

              Ryan Wick, Louise Judd, Claire Gorrie … (2017)
              The Illumina DNA sequencing platform generates accurate but short reads, which can be used to produce accurate but fragmented genome assemblies. Pacific Biosciences and Oxford Nanopore Technologies DNA sequencing platforms generate long reads that can produce complete genome assemblies, but the sequencing is more expensive and error-prone. There is significant interest in combining data from these complementary sequencing technologies to generate more accurate “hybrid” assemblies. However, few tools exist that truly leverage the benefits of both types of data, namely the accuracy of short reads and the structural resolving power of long reads. Here we present Unicycler, a new tool for assembling bacterial genomes from a combination of short and long reads, which produces assemblies that are accurate, complete and cost-effective. Unicycler builds an initial assembly graph from short reads using the de novo assembler SPAdes and then simplifies the graph using information from short and long reads. Unicycler uses a novel semi-global aligner to align long reads to the assembly graph. Tests on both synthetic and real reads show Unicycler can assemble larger contigs with fewer misassemblies than other hybrid assemblers, even when long-read depth and accuracy are low. Unicycler is open source (GPLv3) and available at github.com/rrwick/Unicycler.
              Article 0 comments Cited 2551 times – based on 0 reviews     Review now
                Bookmark
                All references

                Author and article information

                Contributors
                J. Cameron Thrash: Role: Editor
                Journal
                Journal ID (nlm-ta): Microbiol Resour Announc
                Journal ID (iso-abbrev): Microbiol Resour Announc
                Journal ID (hwp): ga
                Journal ID (pmc): mra
                Journal ID (publisher-id): MRA
                Title: Microbiology Resource Announcements
                Publisher: American Society for Microbiology (1752 N St., N.W., Washington, DC )
                ISSN (Electronic): 2576-098X
                Publication date (Electronic): 22 October 2020
                Publication date Collection: October 2020
                Volume: 9
                Issue: 43
                Electronic Location Identifier: e01015-20
                Affiliations
                [a ]Wellcome-Wolfson Institute for Experimental Medicine, Queen's University Belfast, Belfast, United Kingdom
                University of Southern California
                Author notes
                Address correspondence to Miguel A. Valvano, m.valvano@ 123456qub.ac.uk .

                Citation García-Romero I, Valvano MA. 2020. Complete genome sequence of Burkholderia cenocepacia K56-2, an opportunistic pathogen. Microbiol Resour Announc 9:e01015-20. https://doi.org/10.1128/MRA.01015-20.

                Author information
                https://orcid.org/0000-0002-8939-3271
                https://orcid.org/0000-0001-8229-3641
                Article
                Publisher ID: MRA01015-20
                DOI: 10.1128/MRA.01015-20
                PMC ID: 7585848
                PubMed ID: 33093048
                SO-VID: d7cd1a8a-828a-4d8b-bfc8-48bb4304cf42
                Copyright © Copyright © 2020 García-Romero and Valvano.
                License:

                This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International license.

                History
                Date received : 2 September 2020
                Date accepted : 8 October 2020
                Page count
                Figures: 0, Tables: 1, Equations: 0, References: 14, Pages: 2, Words: 1367
                Funding
                Funded by: UKRI | Biotechnology and Biological Sciences Research Council (BBSRC), https://doi.org/10.13039/501100000268;
                Award ID: BB/S006281/1
                Award ID: BB/R022607/1
                Award Recipient :
                Funded by: UKRI | Medical Research Council (MRC), https://doi.org/10.13039/501100000265;
                Award ID: MR/P022480/1
                Award Recipient :
                Categories
                Subject: Genome Sequences
                Custom metadata
                cover-date October 2020

                Data availability:

                Comments

                Comment on this article

                scite_

                Similar content298

                See all similar

                Cited by4

                See all cited by

                Most referenced authors290

                See all reference authors