Hercules: a profile HMM-based hybrid error correction algorithm for long reads
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Summary
Hercules is designed and developed, the first machine learning-based long read error correction algorithm, which shows that Hercules-corrected reads have the highest mapping rate among all competing algorithms and highest accuracy when most of the basepairs of a long read are covered with short reads.
- Type
- article
- Published
- 2017-12-13
- Cited by
- 37
- References
- 42
- Access
- Open access
- OpenAlex
- https://openalex.org/W2775883913
- Semantic Scholar
- https://api.semanticscholar.org/CorpusID:52039741
Keywords
Algorithm, Hidden Markov model, Computer science, Scalability, Word error rate
References
- Jabba: hybrid error correction for long sequencing reads
- The Viterbi Algorithm
- An inequality and associated maximization technique in statistical estimation of probabilistic functions of a Markov process
- Assembling large genomes with single-molecule sequencing and locality-sensitive hashing
- ABySS: a parallel assembler for short read sequence data.
- Error bounds for convolutional codes and an asymptotically optimum decoding algorithm
- Probabilistic error correction for RNA sequencing
- Accurate Whole Human Genome Sequencing using Reversible Terminator Chemistry
- Improving PacBio Long Read Accuracy by Short Read Alignment
- Repetitive DNA and next-generation sequencing: computational challenges and solutions
- Reconstructing complex regions of genomes using long-read sequencing technology
- Limitations of next-generation genome sequence assembly
- SeqAn An efficient, generic C++ library for sequence analysis
- Hidden Markov Models and their Applications in Biological Sequence Analysis
- PREMIER Turbo: Probabilistic error-correction using Markov inference in errored reads using the turbo principle
- The Sequence Alignment/Map format and SAMtools
- A Viterbi algorithm with soft-decision outputs and its applications
- Field guide to next‐generation DNA sequencers
- Real-Time DNA Sequencing from Single Polymerase Molecules
- Using SIMD technology to speed up likelihood computation in HMM-based speech recognition systems
Cited by
- Assessment and correction of errors in DNA sequencing technologies
- A comprehensive evaluation of long read error correction methods
- Apollo: A Sequencing-Technology-Independent, Scalable, and Accurate Assembly Polishing Algorithm
- CONSENT: Scalable self-correction of long reads with multiple sequence alignment
- HyPo: Super Fast & Accurate Polisher for Long Read Genome Assemblies
- TALC: Transcript-level Aware Long Read Correction
- De novo transcriptome of Phakopsora pachyrhizi uncovers putative effector repertoire during infection
- Technology dictates algorithms: recent developments in read alignment
- Long-read error correction: a survey and qualitative comparison
- Computational methods for analysis of single molecule sequencing data
- BlockPolish: accurate polishing of long-read assembly via block divide-and-conquer
- Sequencing DNA with nanopores: Troubles and biases
- Music of metagenomics—a review of its applications, analysis pipeline, and associated tools
- Nanopore sequencing technology, bioinformatics and applications
- A Deep Dive into Genome Assemblies of Non-vertebrate Animals
- Urban Intelligence and Applications: Second International Conference, ICUIA 2020, Taiyuan, China, August 14–16, 2020, Revised Selected Papers
- Simultaneous compression of multiple error-corrected short-read sets for faster data transmission and better de novo assemblies.
- Genome sequence assembly algorithms and misassembly identification methods
- Combination of long-read and short-read sequencing provides comprehensive transcriptome and new insight for Chrysanthemum morifolium ray-floret colorization
- VeChat: correcting errors in long reads using variation graphs
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