{"id":{"repo_id":"mit","oai_identifier":"oai:dspace.mit.edu:1721.1/8931"},"canonical_url":"https://search.dev.ndltd.org/etd/mit/oai:dspace.mit.edu:1721.1/8931","repository":{"repo_id":"mit","name":"MIT","base_url":"https://dspace.mit.edu/oai/request"},"display":{"title":"Software systems for a DNA sequencer","abstract":"The initiative to complete the sequencing of the human genome is bringing the need for high-throughput sequencing capabilities to the forefront. We at the BioMEMS engineering group at the Whitehead Institute are designing and building a new sequencing machine that uses a 384 glass \"chip\" to dramatically increase sequencing rates. This thesis describes the design and implementation of two of the machine's software components. The first is a prototype application for the control of a robot used to automate sample loading. The second is a software filter that allows us to generate quality scores from data processed by Trout using Phred. I present the algorithm used to perform the filtering and show that the results are comparable to the processing of data with the Plan- Phred processing package.","abstract_html":"The initiative to complete the sequencing of the human genome is bringing the need for high-throughput sequencing capabilities to the forefront. We at the BioMEMS engineering group at the Whitehead Institute are designing and building a new sequencing machine that uses a 384 glass "chip" to dramatically increase sequencing rates. This thesis describes the design and implementation of two of the machine's software components. The first is a prototype application for the control of a robot used to automate sample loading. The second is a software filter that allows us to generate quality scores from data processed by Trout using Phred. I present the algorithm used to perform the filtering and show that the results are comparable to the processing of data with the Plan- Phred processing package.","abstract_has_math":false,"creators":["Ait-Ghezala, Ahmed, 1976-"],"institution":"Massachusetts Institute of Technology","degree_name":null,"degree_level":null,"degree_discipline":null,"degree_department":"Massachusetts Institute of Technology. Dept. of Electrical Engineering and Computer Science.","school":null,"contributors":[],"advisors":["Paul Matsudaira."],"committee_chairs":[],"committee_members":[],"year":2000,"date_issued":"2000","date_published":"2000","updated_at":"2026-07-22T22:21:52Z","subjects":["Electrical Engineering and Computer Science."],"languages":["eng"],"rights":["M.I.T. theses are protected by copyright. They may be viewed from this source for any purpose, but reproduction or distribution in any format is prohibited without written permission. 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