Minimum error correction-based haplotype assembly: Considerations for long read data
نویسندگان
چکیده
منابع مشابه
Haplotype reconstruction from SNP fragments by minimum error correction
MOTIVATION Haplotype reconstruction based on aligned single nucleotide polymorphism (SNP) fragments is to infer a pair of haplotypes from localized polymorphism data gathered through short genome fragment assembly. An important computational model of this problem is the minimum error correction (MEC) model, which has been mentioned in several literatures. The model retrieves a pair of haplotype...
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The long-read sequencers from Pacific Bioscience (PacBio) and Oxford Nanopore Technologies (ONT) offer the opportunity to phase mutations multiple kilobases apart directly from sequencing reads. In this study, we used long-range PCR with ONT and PacBio sequencing to phase two variants 9 kb apart in the RET gene. We also re-analysed data from a recent paper which had apparently successfully used...
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A method is presented for incorporating error correction using a minimum distance measure into LR parsers. The method is suitable for use by an automatic parser-generator. State information in the LR parser stack at the point of detection of error is used to generate a set of strings which are potential repairs to the input. A string with least minimum distance from the actual input is chosen a...
متن کاملEnhanced Evolutionary and Heuristic Algorithms for Haplotype Reconstruction Problem Using Minimum Error Correction Model
Construction of two haplotypes from a set of Single Nucleotide Polymorphism (SNP) fragments is referred to as haplotype reconstruction problem. One of the most important computational models for this problem is Minimum Error Correction (MEC). Since MEC is an NP-hard problem, here we propose a heuristic algorithm for haplotype reconstruction problem. The algorithm is Particle Swarm Optimization ...
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ژورنال
عنوان ژورنال: PLOS ONE
سال: 2020
ISSN: 1932-6203
DOI: 10.1371/journal.pone.0234470