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Title: deBGR: an efficient and near-exact representation of the weighted de Bruijn graph

Authors:
 [1];  [1];  [2];  [1]
  1. Department of Computer Science, Stony Brook University, Stony Brook, NY, USA
  2. Department of Computer Science, Stony Brook University, Stony Brook, NY, USA, VMWare, Inc., Palo Alto, CA
Publication Date:
Sponsoring Org.:
USDOE
OSTI Identifier:
1430372
Resource Type:
Published Article
Journal Name:
Bioinformatics
Additional Journal Information:
Journal Name: Bioinformatics Journal Volume: 33 Journal Issue: 14; Journal ID: ISSN 1367-4803
Publisher:
Oxford University Press
Country of Publication:
United Kingdom
Language:
English

Citation Formats

Pandey, Prashant, Bender, Michael A., Johnson, Rob, and Patro, Rob. deBGR: an efficient and near-exact representation of the weighted de Bruijn graph. United Kingdom: N. p., 2017. Web. doi:10.1093/bioinformatics/btx261.
Pandey, Prashant, Bender, Michael A., Johnson, Rob, & Patro, Rob. deBGR: an efficient and near-exact representation of the weighted de Bruijn graph. United Kingdom. doi:10.1093/bioinformatics/btx261.
Pandey, Prashant, Bender, Michael A., Johnson, Rob, and Patro, Rob. Wed . "deBGR: an efficient and near-exact representation of the weighted de Bruijn graph". United Kingdom. doi:10.1093/bioinformatics/btx261.
@article{osti_1430372,
title = {deBGR: an efficient and near-exact representation of the weighted de Bruijn graph},
author = {Pandey, Prashant and Bender, Michael A. and Johnson, Rob and Patro, Rob},
abstractNote = {},
doi = {10.1093/bioinformatics/btx261},
journal = {Bioinformatics},
number = 14,
volume = 33,
place = {United Kingdom},
year = {2017},
month = {7}
}

Journal Article:
Free Publicly Available Full Text
Publisher's Version of Record
DOI: 10.1093/bioinformatics/btx261

Citation Metrics:
Cited by: 3 works
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Works referenced in this record:

An improved data stream summary: the count-min sketch and its applications
journal, April 2005


An Eulerian path approach to DNA fragment assembly
journal, August 2001

  • Pevzner, P. A.; Tang, H.; Waterman, M. S.
  • Proceedings of the National Academy of Sciences, Vol. 98, Issue 17
  • DOI: 10.1073/pnas.171285098

Oases: robust de novo RNA-seq assembly across the dynamic range of expression levels
journal, February 2012


Accurate self-correction of errors in long reads using de Bruijn graphs
journal, June 2016


BinPacker: Packing-Based De Novo Transcriptome Assembly from RNA-seq Data
journal, February 2016


Bridger: a new framework for de novo transcriptome assembly using RNA-seq data
journal, February 2015


Space/time trade-offs in hash coding with allowable errors
journal, July 1970


ABySS: A parallel assembler for short read sequence data
journal, February 2009


How to apply de Bruijn graphs to genome assembly
journal, November 2011

  • Compeau, Phillip E. C.; Pevzner, Pavel A.; Tesler, Glenn
  • Nature Biotechnology, Vol. 29, Issue 11
  • DOI: 10.1038/nbt.2023

Fast search of thousands of short-read sequencing experiments
journal, February 2016

  • Solomon, Brad; Kingsford, Carl
  • Nature Biotechnology, Vol. 34, Issue 3
  • DOI: 10.1038/nbt.3442

Alignment-free sequence comparison--a review
journal, March 2003


Full-length transcriptome assembly from RNA-Seq data without a reference genome
journal, May 2011

  • Grabherr, Manfred G.; Haas, Brian J.; Yassour, Moran
  • Nature Biotechnology, Vol. 29, Issue 7
  • DOI: 10.1038/nbt.1883

These Are Not the K-mers You Are Looking For: Efficient Online K-mer Counting Using a Probabilistic Data Structure
journal, July 2014


Efficient counting of k-mers in DNA sequences using a bloom filter
journal, August 2011


ART: a next-generation sequencing read simulator
journal, December 2011


Scaling metagenome sequence assembly with probabilistic de Bruijn graphs
journal, July 2012

  • Pell, J.; Hintze, A.; Canino-Koning, R.
  • Proceedings of the National Academy of Sciences, Vol. 109, Issue 33
  • DOI: 10.1073/pnas.1121464109

Velvet: Algorithms for de novo short read assembly using de Bruijn graphs
journal, February 2008


Don't thrash: how to cache your hash on flash
journal, July 2012

  • Bender, Michael A.; Zadok, Erez; Farach-Colton, Martin
  • Proceedings of the VLDB Endowment, Vol. 5, Issue 11
  • DOI: 10.14778/2350229.2350275

Improved assembly of noisy long reads by k -mer validation
journal, October 2016

  • Carvalho, Antonio Bernardo; Dupim, Eduardo G.; Goldstein, Gabriel
  • Genome Research, Vol. 26, Issue 12
  • DOI: 10.1101/gr.209247.116

Space-efficient and exact de Bruijn graph representation based on a Bloom filter
journal, January 2013

  • Chikhi, Rayan; Rizk, Guillaume
  • Algorithms for Molecular Biology, Vol. 8, Issue 1
  • DOI: 10.1186/1748-7188-8-22