ArticleBioinformatics (Oxford, England)2017
Kart: a divide-and-conquer algorithm for NGS read alignment.
Article in Bioinformatics (Oxford, England), 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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Who cites it
16 citing papers in PubMed.
- A compressive seeding algorithm in conjunction with reordering-based compression.Bioinformatics (Oxford, England) · 2024Article
- pathMap: a path-based mapping tool for long noisy reads with high sensitivity.Briefings in bioinformatics · 2024Article
- A survey of mapping algorithms in the long-reads era.Genome biology · 2023Review
- Long-read mapping to repetitive reference sequences using Winnowmap2.Nature methods · 2022Article
- Technology dictates algorithms: recent developments in read alignment.Genome biology · 2021Review
- smsMap: mapping single molecule sequencing reads by locating the alignment starting positions.BMC bioinformatics · 2020Article
- SRPRISM (Single Read Paired Read Indel Substitution Minimizer): an efficient aligner for assemblies with explicit guarantees.GigaScience · 2020Article
- Mobile genomics: tools and techniques for tackling transposons.Philosophical transactions of the Royal Society of London. Series B, Biological sciences · 2020Review
- GSAlign: an efficient sequence alignment tool for intra-species genomes.BMC genomics · 2020Article
- SQUAT: a Sequencing Quality Assessment Tool for data quality assessments of genome assemblies.BMC genomics · 2019Article
- Featherweight long read alignment using partitioned reference indexes.Scientific reports · 2019Article
- Minimap2: pairwise alignment for nucleotide sequences.Bioinformatics (Oxford, England) · 2018Article
- Piercing the dark matter: bioinformatics of long-range sequencing and mapping.Nature reviews. Genetics · 2018Review
- DART: a fast and accurate RNA-seq mapper with a partitioning strategy.Bioinformatics (Oxford, England) · 2018Article
- Performance evaluation method for read mapping tool in clinical panel sequencing.Genes & genomics · 2018Article
- Selection of Optimal Bioinformatic Tools and Proper Reference for Reducing the Alignment Error in Targeted Sequencing Data.Journal of medical signals and sensorsArticle
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Authors and funding
2 authors.
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Abstract
motivationNext-generation sequencing (NGS) provides a great opportunity to investigate genome-wide variation at nucleotide resolution. Due to the huge amount of data, NGS applications require very fast and accurate alignment algorithms. Most existing algorithms for read mapping basically adopt seed-and-extend strategy, which is sequential in nature and takes much longer time on longer reads.
resultsWe develop a divide-and-conquer algorithm, called Kart, which can process long reads as fast as short reads by dividing a read into small fragments that can be aligned independently. Our experiment result indicates that the average size of fragments requiring the more time-consuming gapped alignment is around 20 bp regardless of the original read length. Furthermore, it can tolerate much higher error rates. The experiments show that Kart spends much less time on longer reads than other aligners and still produce reliable alignments even when the error rate is as high as 15%. AVAILABILITY AND IMPLEMENTATION: Kart is available at https://github.com/hsinnan75/Kart/ . CONTACT: hsu@iis.sinica.edu.tw. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
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