Error correcting optical mapping data
| dc.contributor.author | Washimkar, Darshan, author | |
| dc.contributor.author | Boucher, Christina, advisor | |
| dc.contributor.author | Pallickara, Sangmi Lee, committee member | |
| dc.contributor.author | Montgomery, Tai, committee member | |
| dc.date.accessioned | 2016-08-18T23:10:17Z | |
| dc.date.available | 2016-08-18T23:10:17Z | |
| dc.date.issued | 2016 | |
| dc.description.abstract | Optical Mapping is a unique system that is capable of producing high-resolution, high-throughput genomic map data that gives information about the structure of a genome (Schwartz et al., Science 1993). Recently it has been used for scaffolding contigs and assembly validation for large-scale sequencing projects — for example, the maize (Zhou et al., PLoS Genetics, 2009), goat (Dong et al., Nature Biotech. 2013), and amborella (Chamala et al., Science 2013) genomes. However, a major impediment in the use of this data is the variety and quantity of the errors in the raw optical mapping data, which are referred to as Rmaps. The challenges associated with using Rmap data—and thus, optical mapping data—is analogous to dealing with insertion and deletions in the alignment of long reads. Moreover, they are arguably harder since the data is integral and susceptible to inaccuracy. We develop cOMet to tackle error correct Rmap data, which to the best of our knowledge is the is the only non-proprietary error correction method. Our results demonstrate that cOMet has high accuracy on simulated E. coli (str. K-12 substr. MG1655) genome. | |
| dc.format.medium | born digital | |
| dc.format.medium | masters theses | |
| dc.identifier | Washimkar_colostate_0053N_13718.pdf | |
| dc.identifier.uri | http://hdl.handle.net/10217/176683 | |
| dc.language | English | |
| dc.language.iso | eng | |
| dc.publisher | Colorado State University. Libraries | |
| dc.relation.ispartof | 2000-2019 | |
| dc.rights | Copyright and other restrictions may apply. User is responsible for compliance with all applicable laws. For information about copyright law, please see https://libguides.colostate.edu/copyright. | |
| dc.subject | multiple alignment | |
| dc.subject | optical mapping | |
| dc.subject | optical map | |
| dc.subject | error correction | |
| dc.title | Error correcting optical mapping data | |
| dc.type | Text | |
| dcterms.rights.dpla | This Item is protected by copyright and/or related rights (https://rightsstatements.org/vocab/InC/1.0/). You are free to use this Item in any way that is permitted by the copyright and related rights legislation that applies to your use. For other uses you need to obtain permission from the rights-holder(s). | |
| thesis.degree.discipline | Computer Science | |
| thesis.degree.grantor | Colorado State University | |
| thesis.degree.level | Masters | |
| thesis.degree.name | Master of Science (M.S.) |
Files
Original bundle
1 - 1 of 1
Loading...
- Name:
- Washimkar_colostate_0053N_13718.pdf
- Size:
- 521.74 KB
- Format:
- Adobe Portable Document Format