ArticleNature communications2019
Accurate high throughput alignment via line sweep-based seed processing.
Article in Nature communications, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 6 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
6 citing papers in PubMed.
- The role of chimeric FAM72B transcripts generated by intergenic mRNA trans-splicing in breast cancer.Functional & integrative genomics · 2025Article
- Smoother: on-the-fly processing of interactome data using prefix sums.Nucleic acids research · 2024Article
- MSV: a modular structural variant caller that reveals nested and complex rearrangements by unifying breakends inferred directly from reads.Genome biology · 2023Article
- Temporal convolutional network for a Fast DNA mutation detection in breast cancer data.PloS one · 2023Article
- From molecules to genomic variations: Accelerating genome analysis via intelligent algorithms and architectures.Computational and structural biotechnology journal · 2022Review
- A performant bridge between fixed-size and variable-size seeding.BMC bioinformatics · 2020Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
3 authors.
Funding
Abstract
Accurate and fast aligners are required to handle the steadily increasing volume of sequencing data. Here we present an approach allowing performant alignments of short reads (Illumina) as well as long reads (Pacific Bioscience, Ultralong Oxford Nanopore), while achieving high accuracy, based on a universal three-stage scheme. It is also suitable for the discovery of insertions and deletions that originate from structural variants. We comprehensively compare our approach to other state-of-the-art aligners in order to confirm its performance with respect to accuracy and runtime. As part of our algorithmic scheme, we introduce two line sweep-based techniques called "strip of consideration" and "seed harmonization". These techniques represent a replacement for chaining and do not rely on any specially tailored data structures. Additionally, we propose a refined form of seeding on the foundation of the FMD-index.
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Registered trials
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.