Filling gaps of genome scaffolds via probabilistic searching optical maps against assembly graph
Background: Optical maps record locations of specific enzyme recognition sites within long genome fragments. This long-distance information enables aligning genome assembly contigs onto optical maps and ordering contigs into scaffolds. The generated scaffolds, however, often contain a large amount o...
Main Authors: | , , , , , , , |
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Format: | Article |
Language: | English |
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BioMed Central Ltd
2021
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Online Access: | View Fulltext in Publisher |
LEADER | 03215nam a2200577Ia 4500 | ||
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001 | 10.1186-s12859-021-04448-2 | ||
008 | 220427s2021 CNT 000 0 und d | ||
020 | |a 14712105 (ISSN) | ||
245 | 1 | 0 | |a Filling gaps of genome scaffolds via probabilistic searching optical maps against assembly graph |
260 | 0 | |b BioMed Central Ltd |c 2021 | |
856 | |z View Fulltext in Publisher |u https://doi.org/10.1186/s12859-021-04448-2 | ||
520 | 3 | |a Background: Optical maps record locations of specific enzyme recognition sites within long genome fragments. This long-distance information enables aligning genome assembly contigs onto optical maps and ordering contigs into scaffolds. The generated scaffolds, however, often contain a large amount of gaps. To fill these gaps, a feasible way is to search genome assembly graph for the best-matching contig paths that connect boundary contigs of gaps. The combination of searching and evaluation procedures might be “searching followed by evaluation”, which is infeasible for long gaps, or “searching by evaluation”, which heavily relies on heuristics and thus usually yields unreliable contig paths. Results: We here report an accurate and efficient approach to filling gaps of genome scaffolds with aids of optical maps. Using simulated data from 12 species and real data from 3 species, we demonstrate the successful application of our approach in gap filling with improved accuracy and completeness of genome scaffolds. Conclusion: Our approach applies a sequential Bayesian updating technique to measure the similarity between optical maps and candidate contig paths. Using this similarity to guide path searching, our approach achieves higher accuracy than the existing “searching by evaluation” strategy that relies on heuristics. Furthermore, unlike the “searching followed by evaluation” strategy enumerating all possible paths, our approach prunes the unlikely sub-paths and extends the highly-probable ones only, thus significantly increasing searching efficiency. © 2021, The Author(s). | |
650 | 0 | 4 | |a algorithm |
650 | 0 | 4 | |a Algorithms |
650 | 0 | 4 | |a Bayes theorem |
650 | 0 | 4 | |a Bayes Theorem |
650 | 0 | 4 | |a contig mapping |
650 | 0 | 4 | |a Contig Mapping |
650 | 0 | 4 | |a Contigs |
650 | 0 | 4 | |a DNA sequence |
650 | 0 | 4 | |a Enzyme recognition |
650 | 0 | 4 | |a Evaluation strategies |
650 | 0 | 4 | |a Filling |
650 | 0 | 4 | |a Filling gaps |
650 | 0 | 4 | |a Gap filling |
650 | 0 | 4 | |a Gap filling |
650 | 0 | 4 | |a Genes |
650 | 0 | 4 | |a genome |
650 | 0 | 4 | |a Genome |
650 | 0 | 4 | |a Genome assembly |
650 | 0 | 4 | |a Genome assembly |
650 | 0 | 4 | |a Optical maps |
650 | 0 | 4 | |a Optical maps |
650 | 0 | 4 | |a Probabilistic search |
650 | 0 | 4 | |a Probabilistic search |
650 | 0 | 4 | |a Probabilistics |
650 | 0 | 4 | |a restriction mapping |
650 | 0 | 4 | |a Restriction Mapping |
650 | 0 | 4 | |a Scaffolding |
650 | 0 | 4 | |a Scaffolding |
650 | 0 | 4 | |a Scaffolds |
650 | 0 | 4 | |a Sequence Analysis, DNA |
700 | 1 | |a Bu, D. |e author | |
700 | 1 | |a Huang, B. |e author | |
700 | 1 | |a Ju, F. |e author | |
700 | 1 | |a Shi, Z. |e author | |
700 | 1 | |a Sun, S. |e author | |
700 | 1 | |a Wang, B. |e author | |
700 | 1 | |a Wei, G. |e author | |
700 | 1 | |a Zhong, Y. |e author | |
773 | |t BMC Bioinformatics |