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Resolving metagenomes usingsingle-molecule linked-readsequencing
KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH).
2018 (English)Independent thesis Advanced level (degree of Master (Two Years)), 20 credits / 30 HE creditsStudent thesis
Abstract [en]

The development of Massively Parallel Sequencing (MPS) has enabled more accurate and lesstime-consuming DNA sequencing. Although MPS technologies are theoretically applicable to allsamples and species, the majority of studies on microorganisms have been conducted on thoseable to be isolated and cultivated in laboratories. In the eld of metagenomics, DNA fromuncultivated environmental samples is analyzed. Whole genome sequencing of such complexsamples poses dicult computational challenges due to the characteristics of metagenomicdata, where one major challenge lies in determining the true origin of high similarity reads. Inaddition, the short-range information acquired from MPS reveals little about how reads fromDNA sequencing t together. Consequently, producing genome drafts from reads generated byMPS remains dicult. Here, the linked-read sequencing technology DB-Seq has been applied tobacterial samples in order to assess its potential in metagenomics. Specically, its performancein retaining long-range information in de novo whole genome assembly has been tested. Theresults obtained in this initial study show great potential of DB-Seq in genome assembly, withsignicantly more contiguous results than conventional methods generate.

Abstract [sv]

Utvecklingen av Massiv Parallel Sekvensering (MPS) har mojliggjort mer korrekt och mindretidskravande DNA sekvensering. Trots att MPS teoretiskt sett kan appliceras pa alla provtyperoch arter, har majoriteten av de studier som utforts pa mikroorganismer varit fokuserade pade som kan isoleras och odlas i laboratorium. Inom amnet metagenomik analyseras DNA franororda miljoprover. Helgenomssekvensering av sadana prover ger upphov till kompliceradeutmaningar for data-analys, dar ett av de storsta problemen ar att bestamma ursprungetav snarlika sekvenseringsresultat. Ytterligare komplikationer uppstar pa grund av den datasom erhalls fran MPS, da denna ej ger information om hur sekvenseringsdata bor placeras iforhallande till varandra. Foljdaktligen ar det svart att producera hopsatta genom utifranMPS-data. I detta projekt har "linked-read"-sekvenseringsteknologin DB-Seq applicerats pabakterieprover for att undersoka metodens potential i metagenomik. Specikt har metodensformaga att bibehalla information om ursprungspositionen av sekvenseringsdata testats i denovo sammansattning av genom. De erhallna resultaten i denna forstagangsstudie tyder pastor potential for DB-Seq i genomsammansattning, med signikant mer sammanhanganderesultatsekvenser an vad konventionella metoder uppvisar.

Place, publisher, year, edition, pages
2018. , p. 42
Keywords [en]
DNA sequencing, linked-read sequencing, DB-Seq, metagenomics, de novo assembly
National Category
Other Engineering and Technologies
Identifiers
URN: urn:nbn:se:kth:diva-231412OAI: oai:DiVA.org:kth-231412DiVA, id: diva2:1228125
Available from: 2018-06-27 Created: 2018-06-27 Last updated: 2018-06-27Bibliographically approved

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CiteExportLink to record
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