Readjoiner: a fast and memory efficient string graph-based sequence assembler.

BMC Bioinformatics
Giorgio Gonnella, Stefan Kurtz

Abstract

Ongoing improvements in throughput of the next-generation sequencing technologies challenge the current generation of de novo sequence assemblers. Most recent sequence assemblers are based on the construction of a de Bruijn graph. An alternative framework of growing interest is the assembly string graph, not necessitating a division of the reads into k-mers, but requiring fast algorithms for the computation of suffix-prefix matches among all pairs of reads. Here we present efficient methods for the construction of a string graph from a set of sequencing reads. Our approach employs suffix sorting and scanning methods to compute suffix-prefix matches. Transitive edges are recognized and eliminated early in the process and the graph is efficiently constructed including irreducible edges only. Our suffix-prefix match determination and string graph construction algorithms have been implemented in the software package Readjoiner. Comparison with existing string graph-based assemblers shows that Readjoiner is faster and more space efficient. Readjoiner is available at http://www.zbh.uni-hamburg.de/readjoiner.

References

Jan 1, 1995·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·E W Myers
Aug 16, 2001·Proceedings of the National Academy of Sciences of the United States of America·P A PevznerM S Waterman
Jan 7, 2004·Genome Research·Mihai PopSteven L Salzberg
Feb 5, 2004·Genome Biology·Stefan KurtzSteven L Salzberg
Oct 6, 2005·Bioinformatics·Eugene W Myers
Dec 18, 2007·Genome Research·Mark J Chaisson, Pavel A Pevzner
Mar 20, 2008·Genome Research·Daniel R Zerbino, Ewan Birney
Mar 3, 2009·Genome Research·Jared T SimpsonInanç Birol
Nov 3, 2009·Nature Methods·John D McPherson
Jun 10, 2010·Bioinformatics·Jared T Simpson, Richard Durbin
Dec 1, 2010·Genome Biology·David R KelleySteven L Salzberg
Dec 15, 2010·Bioinformatics·Marten BoetzerWalter Pirovano
Sep 20, 2011·Genome Research·Dent EarlBenedict Paten
Nov 16, 2011·IEEE/ACM Transactions on Computational Biology and Bioinformatics·Sascha Steinbiss, Stefan Kurtz
Dec 14, 2011·Genome Research·Jared T Simpson, Richard Durbin
Dec 17, 2011·PloS One·Roger BarthelsonSarah Young

❮ Previous
Next ❯

Citations

Nov 21, 2013·Algorithms for Molecular Biology : AMB·Sebastian Deorowicz, Szymon Grabowski
Dec 19, 2013·PLoS Computational Biology·Sara El-MetwallyMohamed Helmy
Sep 4, 2014·Bioinformatics·Ilan Ben-Bassat, Benny Chor
Jan 15, 2014·Briefings in Bioinformatics·Anish Man Singh ShresthaPaul Horton
Mar 10, 2016·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Paola BonizzoniRaffaella Rizzi
Oct 5, 2013·IEEE/ACM Transactions on Computational Biology and Bioinformatics·Gordon GremmeStefan Kurtz
Jun 15, 2015·Bioinformatics·Cheng YuanYanni Sun
Jun 6, 2015·BMC Medical Genomics·Chunyu WangQuan Zou
May 12, 2015·BioMed Research International·Maan Haj Rachid, Qutaibah Malluhi
May 6, 2015·Annual Review of Genomics and Human Genetics·Jared T Simpson, Mihai Pop
Sep 3, 2016·BMC Genomics·Binghang LiuTak-Wah Lam
Jun 25, 2017·Bioinformatics·Giorgio Gonnella, Stefan Kurtz
Jul 18, 2017·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Paola BonizzoniRaffaella Rizzi
Mar 16, 2017·BioMed Research International·Maan Haj Rachid
Nov 16, 2016·PeerJ·Giorgio Gonnella, Stefan Kurtz
Apr 20, 2021·Journal of Bioinformatics and Computational Biology·Zeinab Zare HosseiniAhmad Baraani
Jan 21, 2021·Bioinformatics·Sylwester SwatJacek Blazewicz

❮ Previous
Next ❯

Methods Mentioned

BETA
SGA

Software Mentioned

SSPACE
LEAP
SR
Nucmer
GenomeTools simreads - tool
mmap
GenomeTools
String Graph Assembler ( SGA )
radixsort
GtEncseq

Related Concepts

Trending Feeds

COVID-19

Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.

Blastomycosis

Blastomycosis fungal infections spread through inhaling Blastomyces dermatitidis spores. Discover the latest research on blastomycosis fungal infections here.

Nuclear Pore Complex in ALS/FTD

Alterations in nucleocytoplasmic transport, controlled by the nuclear pore complex, may be involved in the pathomechanism underlying multiple neurodegenerative diseases including Amyotrophic Lateral Sclerosis and Frontotemporal Dementia. Here is the latest research on the nuclear pore complex in ALS and FTD.

Applications of Molecular Barcoding

The concept of molecular barcoding is that each original DNA or RNA molecule is attached to a unique sequence barcode. Sequence reads having different barcodes represent different original molecules, while sequence reads having the same barcode are results of PCR duplication from one original molecule. Discover the latest research on molecular barcoding here.

Chronic Fatigue Syndrome

Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.

Evolution of Pluripotency

Pluripotency refers to the ability of a cell to develop into three primary germ cell layers of the embryo. This feed focuses on the mechanisms that underlie the evolution of pluripotency. Here is the latest research.

Position Effect Variegation

Position Effect Variagation occurs when a gene is inactivated due to its positioning near heterochromatic regions within a chromosome. Discover the latest research on Position Effect Variagation here.

STING Receptor Agonists

Stimulator of IFN genes (STING) are a group of transmembrane proteins that are involved in the induction of type I interferon that is important in the innate immune response. The stimulation of STING has been an active area of research in the treatment of cancer and infectious diseases. Here is the latest research on STING receptor agonists.

Microbicide

Microbicides are products that can be applied to vaginal or rectal mucosal surfaces with the goal of preventing, or at least significantly reducing, the transmission of sexually transmitted infections. Here is the latest research on microbicides.

Related Papers

Proceedings of the National Academy of Sciences of the United States of America
Sante GnerreDavid B Jaffe
Proceedings of the National Academy of Sciences of the United States of America
Pavel PevznerM S Waterman
© 2021 Meta ULC. All rights reserved