2026-09-20T11:56:38Zhttps://dspace.mit.edu/server/oai/requestoai:dspace.mit.edu:1721.1/1180402022-07-19T13:50:03Zcom_1721.1_7582com_1721.1_7581col_1721.1_131023
Bonnie Berger.
Shajii, Ariya (Ariya Reza)
Massachusetts Institute of Technology. Department of Electrical Engineering and Computer Science.
Massachusetts Institute of Technology. Department of Electrical Engineering and Computer Science
2018-09-17T15:54:56Z
2018-09-17T15:54:56Z
2018
2018
http://hdl.handle.net/1721.1/118040
1051459088
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).
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.
by Ariya Shajii.
S.M.
62 pages
eng
Massachusetts Institute of Technology
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.
http://dspace.mit.edu/handle/1721.1/7582
Electrical Engineering and Computer Science.
Fast and accurate alignment of barcoded reads
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<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.</Abstract>
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