ArticleProceedings of the IEEE. Institute of Electrical and Electronics Engineers2017
Short Read Mapping: An Algorithmic Tour.
Article in Proceedings of the IEEE. Institute of Electrical and Electronics Engineers, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 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.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
21 citing papers in PubMed.
- QPL-enabled HTSlib library: accelerating sequence file compression using Intel IAA.Bioinformatics advances · 2026Article
- Key Concepts in Transcriptomics Data Analysis in the Era of Next-Gen Sequencing.Advances in experimental medicine and biology · 2026Review
- Panaln: indexing pangenome for read alignment.Bioinformatics (Oxford, England) · 2025Article
- Block Aligner: an adaptive SIMD-accelerated aligner for sequences and position-specific scoring matrices.Bioinformatics (Oxford, England) · 2023Article
- BLEND: a fast, memory-efficient and accurate mechanism to find fuzzy seed matches in genome analysis.NAR genomics and bioinformatics · 2023Article
- Temporal progress of gene expression analysis with RNA-Seq data: A review on the relationship between computational methods.Computational and structural biotechnology journal · 2023Review
- Quantum computing algorithms: getting closer to critical problems in computational biology.Briefings in bioinformatics · 2022Review
- Performance optimization in DNA short-read alignment.Bioinformatics (Oxford, England) · 2022Review
- Boosting the power of transcriptomics by developing an efficient gene expression profiling approach.Plant biotechnology journal · 2022Article
- ARAMIS: From systematic errors of NGS long reads to accurate assemblies.Briefings in bioinformatics · 2021Article
- Technology dictates algorithms: recent developments in read alignment.Genome biology · 2021Review
- Metagenomics: a path to understanding the gut microbiome.Mammalian genome : official journal of the International Mammalian Genome Society · 2021Review
- Accel-Align: a fast sequence mapper and aligner based on the seed-embed-extend method.BMC bioinformatics · 2021Article
- Review
- Genomic diversity affects the accuracy of bacterial single-nucleotide polymorphism-calling pipelines.GigaScience · 2020Article
- Computational Methods for Strain-Level Microbial Detection in Colony and Metagenome Sequencing Data.Frontiers in microbiology · 2020Review
- Revisiting CRISPR/Cas-mediated crop improvement: Special focus on nutrition.Journal of biosciences · 2020Article
- Review
- Review
- The Current State and Future of CRISPR-Cas9 gRNA Design Tools.Frontiers in pharmacology · 2018Review
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
2 authors.
Funding
Abstract
Ultra-high-throughput next-generation sequencing (NGS) technology allows us to determine the sequence of nucleotides of many millions of DNA molecules in parallel. Accompanied by a dramatic reduction in cost since its introduction in 2004, NGS technology has provided a new way of addressing a wide range of biological and biomedical questions, from the study of human genetic disease to the analysis of gene expression, protein-DNA interactions, and patterns of DNA methylation. The data generated by NGS instruments comprise huge numbers of very short DNA sequences, or 'reads', that carry little information by themselves. These reads therefore have to be pieced together by well-engineered algorithms to reconstruct biologically meaningful measurments, such as the level of expression of a gene. To solve this complex, high-dimensional puzzle, reads must be mapped back to a reference genome to determine their origin Due to sequencing errors and to genuine differences between the reference genome and the individual being sequenced, this mapping process must be tolerant of mismatches, insertions, and deletions. Although optimal alignment algorithms to solve this problem have long been available, the practical requirements of aligning hundreds of millions of short reads to the 3 billion base pair long human genome have stimulated the development of new, more efficient methods, which today are used routinely throughout the world for the analysis of NGS data.
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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.