For Publishers
DiscoveryMetadataPeer reviewHostingPublishing
For Researchers
JoinPublishReviewCollect
Register
Blog
About
Search
Advanced search
My ScienceOpen
Search
For Publishers
For Researchers
Blog
About
33
views
11
references
 Top references
cited by
905
    
0 reviews
 Review
0
comments
 Comment
0
recommends
+1 Recommend
0 collections
    0
    shares
      101
      similar
       All similar
      • Record: found
      • Abstract: found
      • Article: found
      Is Open Access

      NanoPack: visualizing and processing long-read sequencing data

      research-article

      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

          Summary

          Here we describe NanoPack, a set of tools developed for visualization and processing of long-read sequencing data from Oxford Nanopore Technologies and Pacific Biosciences.

          Availability and implementation

          The NanoPack tools are written in Python3 and released under the GNU GPL3.0 License. The source code can be found at https://github.com/wdecoster/nanopack, together with links to separate scripts and their documentation. The scripts are compatible with Linux, Mac OS and the MS Windows 10 subsystem for Linux and are available as a graphical user interface, a web service at http://nanoplot.bioinf.be and command line tools.

          Supplementary information

          Supplementary data are available at Bioinformatics online.

          Related collections

          Most cited references11

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

          The Sequence Alignment/Map format and SAMtools

          Heng Li, Bob Handsaker, Alec Wysoker … (2009)
          Summary: The Sequence Alignment/Map (SAM) format is a generic alignment format for storing read alignments against reference sequences, supporting short and long reads (up to 128 Mbp) produced by different sequencing platforms. It is flexible in style, compact in size, efficient in random access and is the format in which alignments from the 1000 Genomes Project are released. SAMtools implements various utilities for post-processing alignments in the SAM format, such as indexing, variant caller and alignment viewer, and thus provides universal tools for processing read alignments. Availability: http://samtools.sourceforge.net Contact: rd@sanger.ac.uk
          Article 0 comments Cited 13589 times – based on 0 reviews     Review now
            Bookmark
            • Record: found
            • Abstract: not found
            • Article: not found

            Matplotlib: A 2D Graphics Environment

            John Hunter (2007)
            Article 0 comments Cited 5352 times – based on 0 reviews     Review now
              Bookmark
              • Record: found
              • Abstract: not found
              • Article: not found

              The NumPy Array: A Structure for Efficient Numerical Computation

              Stefan van der Walt, S. Chris Colbert, Gael Varoquaux (2011)
              Article 0 comments Cited 1529 times – based on 0 reviews     Review now
                Bookmark
                All references

                Author and article information

                Contributors
                Bonnier Berger: Role: Associate Editor
                Journal
                Journal ID (nlm-ta): Bioinformatics
                Journal ID (iso-abbrev): Bioinformatics
                Journal ID (publisher-id): bioinformatics
                Title: Bioinformatics
                Publisher: Oxford University Press
                ISSN (Print): 1367-4803
                ISSN (Electronic): 1367-4811
                Publication date (Print): 01 August 2018
                Publication date (Electronic): 14 March 2018
                Publication date PMC-release: 14 March 2018
                Volume: 34
                Issue: 15
                Pages: 2666-2669
                Affiliations
                [1 ]Neurodegenerative Brain Diseases Group, VIB & University of Antwerp, Antwerp, Belgium
                [2 ]Bioinformatics, Neuromics Support Facility, Center for Molecular Neurology, VIB & University of Antwerp, Antwerp, Belgium
                [3 ]Department of Biomolecular Engineering and Bioinformatics, University of California Santa Cruz, Santa Cruz, CA, USA
                Author notes
                To whom correspondence should be addressed. Email: wouter.decoster@ 123456molgen.vib-ua.be
                Author information
                http://orcid.org/0000-0002-5248-8197
                Article
                Publisher ID: bty149
                DOI: 10.1093/bioinformatics/bty149
                PMC ID: 6061794
                PubMed ID: 29547981
                SO-VID: 1c654121-4b58-42a6-9b85-ba781fb58a0a
                Copyright © © The Author(s) 2018. Published by Oxford University Press.
                License:

                This is an Open Access article distributed under the terms of the Creative Commons Attribution License ( http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.

                History
                Date received : 02 January 2018
                Date revision received : 19 February 2018
                Date accepted : 12 March 2018
                Page count
                Pages: 4
                Funding
                Funded by: VIB 10.13039/501100004727
                Funded by: Flanders Institute for Biotechnology, Belgium
                Funded by: University of Antwerp 10.13039/501100007660
                Funded by: Flanders Agency for Innovation and Entrepreneurship
                Funded by: NSF 10.13039/100000001
                Funded by: DGE 10.13039/100000082
                Award ID: 1339067
                Categories
                Subject: Applications Notes
                Subject: Sequence Analysis

                ScienceOpen disciplines: Bioinformatics & Computational biology
                Data availability:
                ScienceOpen disciplines: Bioinformatics & Computational biology

                Comments

                Comment on this article

                scite_

                Similar content101

                See all similar

                Cited by1,007

                See all cited by

                Most referenced authors775

                See all reference authors