ArticleAlgorithms for molecular biology : AMB2016
Jabba: hybrid error correction for long sequencing reads.
Article in Algorithms for molecular biology : AMB, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 28 papers.
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Who cites it
28 citing papers in PubMed.
- Review
- Genome assembly in the telomere-to-telomere era.Nature reviews. Genetics · 2024Review
- NmTHC: a hybrid error correction method based on a generative neural machine translation model with transfer learning.BMC genomics · 2024Article
- Nanopore DNA sequencing technologies and their applications towards single-molecule proteomics.Nature chemistry · 2024Review
- Genomic resources for the Yellowfin tuna Thunnus albacares.Molecular biology reports · 2024Article
- DeepCorr: a novel error correction method for 3GS long reads based on deep learning.PeerJ. Computer science · 2024Article
- Genome sequence assembly algorithms and misassembly identification methods.Molecular biology reports · 2022Review
- Computational graph pangenomics: a tutorial on data structures and their applications.Natural computing · 2022Article
- The Statistics ofJournal of computational biology : a journal of computational molecular cell biology · 2022Article
- MONI: A Pangenomic Index for Finding Maximal Exact Matches.Journal of computational biology : a journal of computational molecular cell biology · 2022Article
- Lerna: transformer architectures for configuring error correction tools for short- and long-read genome sequencing.BMC bioinformatics · 2022Article
- Third-Generation Sequencing: The Spearhead towards the Radical Transformation of Modern Genomics.Life (Basel, Switzerland) · 2021Review
- Nanopore sequencing technology, bioinformatics and applications.Nature biotechnology · 2021Review
- Scalable long read self-correction and assembly polishing with multiple sequence alignment.Scientific reports · 2021Article
- Ratatosk: hybrid error correction of long reads enables accurate variant calling and assembly.Genome biology · 2021Article
- A comprehensive evaluation of long read error correction methods.BMC genomics · 2020Review
- A hybrid correcting method considering heterozygous variations by a comprehensive probabilistic model.BMC genomics · 2020Article
- GraphAligner: rapid and versatile sequence-to-graph alignment.Genome biology · 2020Article
- Accurate determination of node and arc multiplicities in de bruijn graphs using conditional random fields.BMC bioinformatics · 2020Article
- ELECTOR: evaluator for long reads correction methods.NAR genomics and bioinformatics · 2020Article
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7 authors.
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No grant is acknowledged in the PubMed record.
Abstract
backgroundThird generation sequencing platforms produce longer reads with higher error rates than second generation technologies. While the improved read length can provide useful information for downstream analysis, underlying algorithms are challenged by the high error rate. Error correction methods in which accurate short reads are used to correct noisy long reads appear to be attractive to generate high-quality long reads. Methods that align short reads to long reads do not optimally use the information contained in the second generation data, and suffer from large runtimes. Recently, a new hybrid error correcting method has been proposed, where the second generation data is first assembled into a de Bruijn graph, on which the long reads are then aligned.
resultsIn this context we present Jabba, a hybrid method to correct long third generation reads by mapping them on a corrected de Bruijn graph that was constructed from second generation data. Unique to our method is the use of a pseudo alignment approach with a seed-and-extend methodology, using maximal exact matches (MEMs) as seeds. In addition to benchmark results, certain theoretical results concerning the possibilities and limitations of the use of MEMs in the context of third generation reads are presented.
conclusionJabba produces highly reliable corrected reads: almost all corrected reads align to the reference, and these alignments have a very high identity. Many of the aligned reads are error-free. Additionally, Jabba corrects reads using a very low amount of CPU time. From this we conclude that pseudo alignment with MEMs is a fast and reliable method to map long highly erroneous sequences on a de Bruijn graph.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.