SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing.

Journal of Computational Biology : a Journal of Computational Molecular Cell Biology
Anton BankevichPavel A Pevzner

Abstract

The lion's share of bacteria in various environments cannot be cloned in the laboratory and thus cannot be sequenced using existing technologies. A major goal of single-cell genomics is to complement gene-centric metagenomic data with whole-genome assemblies of uncultivated organisms. Assembly of single-cell data is challenging because of highly non-uniform read coverage as well as elevated levels of sequencing errors and chimeric reads. We describe SPAdes, a new assembler for both single-cell and standard (multicell) assembly, and demonstrate that it improves on the recently released E+V-SC assembler (specialized for single-cell data) and on popular assemblers Velvet and SoapDeNovo (for multicell data). SPAdes generates single-cell assemblies, providing information about genomes of uncultivatable bacteria that vastly exceeds what may be obtained via traditional metagenomics studies. SPAdes is available online ( http://bioinf.spbau.ru/spades ). It is distributed as open source software.

References

Jan 1, 1995·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·R M Idury, M S Waterman
Jul 27, 2001·Bioinformatics·P A Pevzner, H Tang
Aug 16, 2001·Proceedings of the National Academy of Sciences of the United States of America·P A PevznerM S Waterman
Sep 3, 2004·Genome Research·Pavel A PevznerGlenn Tesler
Feb 11, 2005·Chemical Reviews·Stephan A Sieber, Mohamed A Marahiel
Jun 3, 2006·Science·Steven R GillKaren E Nelson
Apr 21, 2007·Molecular & Cellular Proteomics : MCP·Nuno BandeiraPavel A Pevzner
Jul 11, 2007·Proceedings of the National Academy of Sciences of the United States of America·Yann MarcyStephen R Quake
Dec 18, 2007·Genome Research·Mark J Chaisson, Pavel A Pevzner
Mar 15, 2008·Genome Research·Jonathan ButlerDavid B Jaffe
Mar 20, 2008·Genome Research·Daniel R Zerbino, Ewan Birney
Jun 14, 2008·Current Opinion in Microbiology·Thomas IshoeyRoger S Lasken
Dec 6, 2008·Genome Research·Mark J ChaissonPavel A Pevzner
Dec 9, 2008·Nature Biotechnology·Nuno BandeiraJennie R Lill
Feb 28, 2009·BMC Bioinformatics·Mohammad Sajjad HossainSteven Skiena
Mar 3, 2009·Genome Research·Jared T SimpsonInanç Birol
Jul 11, 2009·Science·Jesse W-H Li, John C Vederas
Sep 3, 2009·PloS One·Sébastien RodrigueSallie W Chisholm
Mar 12, 2010·Genome Biology·David R Kelley, Steven L Salzberg
Apr 30, 2010·PloS One·Tanja WoykeJan-Fang Cheng
Aug 26, 2010·Bioinformatics·Son K Pham, Pavel A Pevzner
Dec 1, 2010·Genome Biology·David R KelleySteven L Salzberg
Dec 1, 2010·Bioinformatics·Lucian IlieSilvana Ilie
Dec 21, 2010·Nature Biotechnology·H Christina FanStephen R Quake
Dec 29, 2010·Proceedings of the National Academy of Sciences of the United States of America·Sante GnerreDavid B Jaffe
Mar 15, 2011·Nature·Nicholas NavinMichael Wigler
Jun 21, 2011·Bioinformatics·Paul MedvedevPavel Pevzner
Sep 13, 2011·Applied and Environmental Microbiology·Noha H YoussefMostafa S Elshahed
Sep 20, 2011·Nature Biotechnology·Hamidreza ChitsazRoger S Lasken
Oct 18, 2011·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Paul MedvedevPavel Pevzner
Nov 15, 2011·Nature Biotechnology·Piero DalerbaStephen R Quake

❮ Previous
Next ❯

Citations

Nov 10, 2013·Nature Protocols·Helena M B Seth-SmithNicholas R Thomson
Jul 19, 2012·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Son K PhamMax A Alekseyev
Oct 8, 2013·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Sergey NurkPavel A Pevzner
Jun 13, 2012·Bioinformatics·Roy RonenPavel Pevzner
Feb 21, 2013·Bioinformatics·Alexey GurevichGlenn Tesler
May 15, 2013·Bioinformatics·Tanja MagocSteven L Salzberg
Aug 31, 2013·Bioinformatics·Aleksey V ZiminJames A Yorke
Mar 26, 2013·Genome Research·Helena M B Seth-SmithNicholas R Thomson
May 25, 2013·Genome Announcements·Jorge Ibarra CaballeroNed Tisserat
Dec 29, 2013·Genome Announcements·Dongping WangLeland S Pierson
Dec 21, 2013·Genome Announcements·Yu-Chieh LiaoChao Agnes Hsiung
Feb 26, 2014·BMC Bioinformatics·Hayssam SoueidanMacha Nikolski
Feb 13, 2013·BMC Genomics·Sergey I NikolenkoMax A Alekseyev
Sep 17, 2013·Genome Biology·Sergey KorenAdam M Phillippy
Mar 7, 2014·PloS One·Philippe M HauserGaudenz M Hafen
Apr 12, 2014·Genome Announcements·Olivier CroceMichel Drancourt
Apr 20, 2014·Genome Announcements·Olivier CroceMichel Drancourt
Mar 13, 2014·Bioinformatics·Gianmauro CuccuruGiorgio Fotia
May 3, 2014·Genome Announcements·Olivier CroceMichel Drancourt
Feb 22, 2014·Genome Announcements·Camila ValenzuelaCarlos A Santiviago
May 9, 2014·Genome Announcements·Joshua QuickNicholas J Loman
May 9, 2014·Genome Announcements·Olivier CroceMichel Drancourt
May 31, 2014·Genome Announcements·Mohamed SassiMichel Drancourt
Jun 3, 2014·BMC Bioinformatics·Sergey KorenAdam M Phillippy
Jan 18, 2014·Genome Announcements·Victoriya Y ShtratnikovaMarina V Donova

❮ Previous
Next ❯

Methods Mentioned

BETA
Single-Cell Sequencing
MDA

Software Mentioned

SOAPdenovo
SC
EULER
IDBA
SPAdes
Velvet
Quake
DeclareMathSizes
; SC
SR

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.