Help Login Create account

Data released on December 17, 2015

Supporting software for OPTIMA, a tool for sensitive and accurate whole-genome alignment of error-prone genomic maps by combinatorial indexing and technology-agnostic statistical analysis.

Hillmer, A, M; Teo, A, S; Verzotto, D; Nagarajan, N (2015): Supporting software for OPTIMA, a tool for sensitive and accurate whole-genome alignment of error-prone genomic maps by combinatorial indexing and technology-agnostic statistical analysis. GigaScience Database. http://dx.doi.org/10.5524/100165 RIS BibTeX Text

Resolution of complex repeat structures and rearrangements in the assembly and analysis of large eukaryotic genomes is often aided by a combination of high-throughput sequencing and genome mapping technologies (e.g. optical restriction mapping). In particular, mapping technologies can generate sparse maps of large DNA fragments (150 kbp–2 Mbp) and thus provide a unique source of information for disambiguating complex rearrangements in cancer genomes. Despite their utility, combining high-throughput sequencing and mapping technologies has been challenging due to the lack of efficient and sensitive map alignment algorithms for robustly aligning error-prone maps to sequences.
We introduce a novel seed-and-extend glocal alignment method, called OPTIMA (and a sliding-window extension for overlap alignment, called OPTIMA-Overlap), that is the first to be able to create indexes for continuous-valued mapping data while accounting for mapping errors. We also present a novel statistical model, agnostic to technology-dependent error rates, for conservatively evaluating the significance of alignments without relying on expensive permutation-based tests.

Contact Submitter

Related manuscripts:

doi:10.1186/s13742-015-0106-1
doi:10.1186/s13742-016-0110-0

Related datasets:

doi:10.5524/100165 IsSupplementedBy doi:10.5524/100182

Additional information:

https://github.com/verznet/OPTIMA

http://www.davideverzotto.it/research/OPTIMA/

Keywords:

optical mapping genomic mapping glocal alignment overlap alignment map-to-sequence alignment 

Software, Genome-Mapping

/images/uploads/image_upload/Images_250.png

Files: (FTP site) Table Settings

Columns:

File Description
Sample ID
File Type
File Format
Size
Release Date
Download Link
File Attributes

File NameSample IDFile TypeFile FormatSizeRelease Date 
OtherUNKNOWN537.44 KB2015-12-04
OtherUNKNOWN1.61 MB2015-12-04
OtherUNKNOWN57.81 KB2015-12-04
OtherUNKNOWN396.01 KB2015-12-04
OtherUNKNOWN2.47 MB2015-12-04
OtherUNKNOWN11.09 MB2015-12-04
OtherUNKNOWN1.6 KB2015-12-04
OtherUNKNOWN902.01 KB2015-12-04
OtherUNKNOWN5.01 MB2015-12-04
OtherUNKNOWN22.91 MB2015-12-04
Displaying 1-10 of 24 File(s).

History:

+

Other datasets you might like: