dipSPAdes: Assembler for Highly Polymorphic Diploid Genomes

Journal of Computational Biology : a Journal of Computational Molecular Cell Biology
Yana SafonovaPavel A Pevzner

Abstract

While the number of sequenced diploid genomes have been steadily increasing in the last few years, assembly of highly polymorphic (HP) diploid genomes remains challenging. As a result, there is a shortage of tools for assembling HP genomes from the next generation sequencing (NGS) data. The initial approaches to assembling HP genomes were proposed in the pre-NGS era and are not well suited for NGS projects. To address this limitation, we developed the first de Bruijn graph assembler, dipSPAdes, for HP genomes that significantly improves on the state-of-the-art assemblers for HP diploid genomes.

References

Aug 16, 2001·Proceedings of the National Academy of Sciences of the United States of America·P A PevznerM S Waterman
Jan 10, 2002·Genome Research·Serafim BatzoglouEric S Lander
Jul 5, 2002·Genome Research·Kathryn A SwanMichael R Cancilla
Jul 27, 2002·Science·Samuel AparicioSydney Brenner
Jul 3, 2004·Genome Research·Aaron C E DarlingNicole T Perna
Jul 30, 2005·Computational Biology and Chemistry·Yu-Ying ZhaoXiang-Sun Zhang
Aug 4, 2005·Genome Research·Jade P VinsonEric S Lander
Mar 20, 2008·Genome Research·Daniel R Zerbino, Ewan Birney
Aug 5, 2008·Genome Research·Vikas BansalVineet Bafna
Nov 10, 2011·Nature Biotechnology·Phillip E C CompeauGlenn Tesler
Dec 8, 2011·Genome Research·Steven L SalzbergJames A Yorke
Apr 18, 2012·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Anton BankevichPavel A Pevzner
Jun 16, 2012·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Derek Aguiar, Sorin Istrail
Feb 21, 2013·Bioinformatics·Alexey GurevichGlenn Tesler
May 15, 2013·Bioinformatics·Tanja MagocSteven L Salzberg
Jun 17, 2014·Bioinformatics·Andrey D PrjibelskiPavel A Pevzner

❮ Previous
Next ❯

Citations

Nov 7, 2016·Virus Research·Sylvie RatoAngela Ciuffi
Mar 17, 2017·Genome Research·Sergey NurkPavel A Pevzner
Apr 25, 2018·PLoS Biology·Reuben W NowellTimothy G Barraclough
Aug 12, 2017·Genome Announcements·Rose WaldronDavid A Fitzpatrick
Aug 1, 2018·PLoS Biology·Michael EitelGert Wörheide
Mar 24, 2016·Nature Communications·Sesh A SundararamanBeatrice H Hahn
Apr 18, 2019·Bioinformatics·Jasmijn A Baaijens, Alexander Schönhuth
Dec 14, 2019·Bioinformatics·Cinta PeguerolesToni Gabaldón
Apr 18, 2020·Biological Reviews of the Cambridge Philosophical Society·Miguel A Naranjo-Ortiz, Toni Gabaldón
Apr 28, 2018·Genome Announcements·Miguel A Naranjo-OrtízToni Gabaldón
Apr 6, 2019·Microbiology Resource Announcements·João TrovãoAntónio Portugal
Dec 1, 2018·BMC Bioinformatics·Michael J RoachAnthony R Borneman
Oct 6, 2018·Genome Biology·Alexandre SouvorovDavid J Lipman
Jun 6, 2020·Current Biology : CB·Jacob L SteenwykAntonis Rokas
Mar 1, 2019·G3 : Genes - Genomes - Genetics·Andrea MinioDario Cantu
Mar 8, 2021·Genomics, Proteomics & Bioinformatics·Jie WangRachel Lockridge Mueller
Jun 16, 2021·DNA Research : an International Journal for Rapid Publication of Reports on Genes and Genomes·Verónica MixãoToni Gabaldón

❮ Previous
Next ❯

Datasets Mentioned

BETA
SRX113442

Software Mentioned

QUAST
dip SPA
SPAdes assembler
SPA des
MAUVE
dipSPAdes
dip SPA des
MM
ConsensusGraph
Velvet

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.