Fast and accurate alignment of barcoded reads
Name
1051459088-MIT.pdf
Description
Full printable version
Size
5.52 MB
Format
Adobe PDF
Checksum (MD5)
ac04026a25413cd41922256449e08042
Author(s)
Shajii, Ariya (Ariya Reza)
Advisor(s)
Bonnie Berger.
Date Issued
2018
Publisher
Massachusetts Institute of Technology
Abstract
Over the last few years, we have seen the emergence of several so-called "third-generation" sequencing platforms, which improve on standard short-read sequencing that has thus far been at the center of next-generation sequencing. While technologies developed by Pacific Biosciences and Oxford Nanopore accomplish this goal by producing physically longer reads, several other technologies take an alternate route by instead producing "barcoded reads", including 10x Genomics' Chromium platform and Illumina's TruSeq Synthetic Long-Read platform. With barcoded reads, long-range information is captured by the barcodes, which identify source DNA fragments. As with all sequencing data, alignment of barcoded reads is the first step in nearly all analyses, and therefore plays a central role. Here, we design and validate improved alignment algorithms for barcoded sequencing data, which enable improved downstream analyses like phasing and genotyping, and additionally uncover variants in regions containing nearby homologous elements that go undetected by other methods.
Description
Thesis: S.M., Massachusetts Institute of Technology, Department of Electrical Engineering and Computer Science, 2018.
Cataloged from PDF version of thesis.
Includes bibliographical references (pages 57-62).
Subjects
Electrical Engineering and Computer Science.
MIT Department
Massachusetts Institute of Technology. Department of Electrical Engineering and Computer Science
Terms of Use
MIT theses are protected by copyright. They may be viewed, downloaded, or printed from this source but further reproduction or distribution in any format is prohibited without written permission.
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