OPTIMA: sensitive and accurate whole-genome alignment of error-prone genomic maps by combinatorial indexing and technology-agnostic statistical analysis

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• 作者：Davide Verzotto ; Audrey S. M. Teo ; Axel M. Hillmer ; Niranjan Nagarajan
• 关键词：Optical mapping ; Genomic mapping ; Glocal alignment ; Overlap alignment ; Map ; to ; sequence alignment
• 刊名：GigaScience
• 出版年：2016
• 出版时间：December 2016
• 年：2016
• 卷：5
• 期：1
• 全文大小：2,825 KB
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  25.Teo ASM, Verzotto D, Yao F, Nagarajan N, Hillmer AM. Single-molecule optical genome mapping of a human HapMap and a colorectal cancer cell line. GigaScience. 2015; 4:65. doi:10.​1186/​s13742-015-0106-1 .PubMed PubMedCentral CrossRef
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  29.Verzotto D, Teo ASM, Hillmer AM, Nagarajan N. 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; 2015. GigaScience Database. doi:10.​5524/​100165 .
  30.Teo ASM, Verzotto D, Yao F, Nagarajan N, Hillmer AM. Supporting single-molecule optical genome mapping data from human HapMap and colorectal cancer cell lines; 2015. GigaScience Database. doi:10.​5524/​100182 .
  
• 作者单位：Davide Verzotto (1)
  Audrey S. M. Teo (2)
  Axel M. Hillmer (2)
  Niranjan Nagarajan (1)
  
  1. Computational and Systems Biology, Genome Institute of Singapore, 60 Biopolis Street, Singapore, 138672, Singapore
  2. Cancer Therapeutics and Stratified Oncology, Genome Institute of Singapore, 60 Biopolis Street, Singapore, 138672, Singapore
  
• 刊物主题：Bioinformatics; Computational Biology/Bioinformatics; Computer Appl. in Life Sciences; Proteomics; Data Mining and Knowledge Discovery;
• 出版者：BioMed Central
• ISSN：2047-217X

文摘

Background 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 (for example, optical restriction mapping). In particular, mapping technologies can generate sparse maps of large DNA fragments (150 kilo base pairs (kbp) to 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 because of the lack of efficient and sensitive map-alignment algorithms for robustly aligning error-prone maps to sequences.