Ändra sökning
RefereraExporteraLänk till posten
Permanent länk

Direktlänk
Referera
Referensformat
  • apa
  • ieee
  • modern-language-association-8th-edition
  • vancouver
  • Annat format
Fler format
Språk
  • de-DE
  • en-GB
  • en-US
  • fi-FI
  • nn-NO
  • nn-NB
  • sv-SE
  • Annat språk
Fler språk
Utmatningsformat
  • html
  • text
  • asciidoc
  • rtf
BESST - Efficient scaffolding of large fragmented assemblies
Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för biokemi och biofysik. Stockholms universitet, Science for Life Laboratory (SciLifeLab).
Visa övriga samt affilieringar
2014 (Engelska)Ingår i: BMC Bioinformatics, ISSN 1471-2105, E-ISSN 1471-2105, Vol. 15, artikel-id 281Artikel i tidskrift (Refereegranskat) Published
Abstract [en]

Background

The use of short reads from High Throughput Sequencing (HTS) techniques is now commonplace in de novo assembly. Yet, obtaining contiguous assemblies from short reads is challenging, thus making scaffolding an important step in the assembly pipeline. Different algorithms have been proposed but many of them use the number of read pairs supporting a linking of two contigs as an indicator of reliability. This reasoning is intuitive, but fails to account for variation in link count due to contig features.

We have also noted that published scaffolders are only evaluated on small datasets using output from only one assembler. Two issues arise from this. Firstly, some of the available tools are not well suited for complex genomes. Secondly, these evaluations provide little support for inferring a software’s general performance. 

Results

We propose a new algorithm, implemented in a tool called BESST, which can scaffold genomes of all sizes and complexities and was used to scaffold the genome of P. abies (20 Gbp). We performed a comprehensive comparison of BESST against the most popular stand-alone scaffolders on a large variety of datasets. Our results confirm that some of the popular scaffolders are not practical to run on complex datasets. Furthermore, no single stand-alone scaffolder outperforms the others on all datasets. However, BESST fares favorably to the other tested scaffolders on GAGE datasets and, moreover, outperforms the other methods when library insert size distribution is wide.

Conclusion

We conclude from our results that information sources other than the quantity of links, as is commonly used, can provide useful information about genome structure when scaffolding. 

Ort, förlag, år, upplaga, sidor
2014. Vol. 15, artikel-id 281
Nyckelord [en]
Genome assembly, Scaffolding, Genome analysis, Mate pair next-generation sequencing
Nationell ämneskategori
Bioinformatik (beräkningsbiologi)
Identifikatorer
URN: urn:nbn:se:su:diva-106778DOI: 10.1186/1471-2105-15-281ISI: 000341198900001OAI: oai:DiVA.org:su-106778DiVA, id: diva2:738943
Forskningsfinansiär
Swedish e‐Science Research CenterVetenskapsrådet, 2010-4634Knut och Alice Wallenbergs StiftelseTillgänglig från: 2014-08-19 Skapad: 2014-08-19 Senast uppdaterad: 2018-03-14Bibliografiskt granskad

Open Access i DiVA

fulltext(208 kB)180 nedladdningar
Filinformation
Filnamn FULLTEXT01.pdfFilstorlek 208 kBChecksumma SHA-512
a841a1d1e9577f55ac82407df881551fbe4caf4c304530c845e47bf8578046437521009b663abe5cb20d2151bb206908b5c4313c08addef2e5e7c6ccbc6f2ce4
Typ fulltextMimetyp application/pdf

Övriga länkar

Förlagets fulltext

Sök vidare i DiVA

Av författaren/redaktören
Arvestad, Lars
Av organisationen
Institutionen för biokemi och biofysikScience for Life Laboratory (SciLifeLab)Numerisk analys och datalogi (NADA)
I samma tidskrift
BMC Bioinformatics
Bioinformatik (beräkningsbiologi)

Sök vidare utanför DiVA

GoogleGoogle Scholar
Totalt: 180 nedladdningar
Antalet nedladdningar är summan av nedladdningar för alla fulltexter. Det kan inkludera t.ex tidigare versioner som nu inte längre är tillgängliga.

doi
urn-nbn

Altmetricpoäng

doi
urn-nbn
Totalt: 120 träffar
RefereraExporteraLänk till posten
Permanent länk

Direktlänk
Referera
Referensformat
  • apa
  • ieee
  • modern-language-association-8th-edition
  • vancouver
  • Annat format
Fler format
Språk
  • de-DE
  • en-GB
  • en-US
  • fi-FI
  • nn-NO
  • nn-NB
  • sv-SE
  • Annat språk
Fler språk
Utmatningsformat
  • html
  • text
  • asciidoc
  • rtf