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Compression of Short Read data sets

Mistereggen, Eirik
Master thesis
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Mistereggen.pdf (1.028Mb)
Year
2011
Permanent link
http://urn.nb.no/URN:NBN:no-29852

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  • Institutt for informatikk [3652]
Abstract
Neste-generasjons sekvensering gir en stor mengde data i form av Short Reads. I denne oppgaven presenterer vi muligheter for å komprimere disse dataene ved hjelp av differensiering. Vi ser på to tilfeller; først komprimering av ubehandlede data med differensiering internt, så komprimering av data som er kartlagt mot et referansegenom. Vi viser resultater hvor vi i de fleste tilfellene oppnår signifikant komprimering.
 
With the rapid progression in the field of DNA sequencing, an appreciable

part of total costs has moved from the wet lab to the server room. New

platforms are generating data that increases in size faster than the storage

capacity. More effective compression than generic techniques is possible due

to the traits inhabited by the sequencing output. In this thesis we look

at using diff erential compression both for raw unmapped reads and reads

that been mapped to a reference genome. For the aligned reads this means

using a reference-based solution where the information in the reads is stored

as a di fferencing against a reference library. For the unaligned reads we

use an intra-frame diff erencing similar to frame-to-frame approach in video

compression. With this approach we are able to show a proof-of-concept

where signficant compression rates are attainable in both cases.
 
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