ArticleHuman genome variation2024
Comparative evaluation of SNVs, indels, and structural variations detected with short- and long-read sequencing data.
Article in Human genome variation, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 38 papers.
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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
38 citing papers in PubMed.
- Pangenomes aid accurate detection of large insertions and deletions from targeted sequencing: the case of cardiomyopathies.Genome medicine · 2026Article
- Long-Read Sequencing in CKD Diagnostics: Breaking Genomic Barriers and Expanding Global Inclusion.Kidney international reports · 2026Review
- Concordance Between Fragment Analysis and Next-Generation Sequencing in Identification of Non-Standard CALR Indels.International journal of laboratory hematology · 2026Article
- Long-read sequencing for neurological disorders: opportunities, challenges, and future directions.Neurological sciences : official journal of the Italian Neurological Society and of the Italian Society of Clinical Neurophysiology · 2026Review
- DNA Replication Errors Drive Genome-Wide Small Inverted Triplication Dynamics.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Genomic Variability of the HCT116 Cell Line Identified Using Oxford Nanopore Sequencing.International journal of molecular sciences · 2026Article
- Decoding DNA metabolism and its clinical relevance through the lens of high-throughput sequencing assays.Medical review (2021) · 2026Review
- Manual validation finds ultra-long-read sequencing best enables faithful, population-level structural variant calling in Drosophila melanogaster euchromatin with nanopore.G3 (Bethesda, Md.) · 2026Article
- Long-Read Haplotype Phasing Resolves Allelic Configuration as a Missing Layer of Precision Oncology.medRxiv : the preprint server for health sciences · 2026Article
- Proof-of-concept study for the detection of somatic structural variant driver alterations using HiFi long-read sequencing in a pediatric leukemia cohort.NPJ genomic medicine · 2026Article
- Benchmarking of sequencing technologies defines optimal strategies for genetic variants detection in a human genome.Genome biology · 2026Article
- Integrating Long-Read Structural Variant Analysis with single-nucleus RNA-seq to Elucidate Gene Expression Effects in Disease.bioRxiv : the preprint server for biology · 2026Article
- An integrated multiple analysis reveals the genetic information associated with root-related traits in wheat (Triticum aestivum L.).TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2026Article
- GWAS SVatalog: a visualization tool to aid fine-mapping of GWAS loci with structural variations.Heredity · 2026Article
- ANOMALY: a Snakemake pipeline for identifying NuMTs from long-read sequencing data.NAR genomics and bioinformatics · 2026Article
- The impact of AI on modern oncology from early detection to personalized cancer treatment.NPJ precision oncology · 2026Review
- Neurofibromin 1 (International journal of molecular sciences · 2026Article
- Article
- Molecular QTL are enriched for structural variants in a cattle long-read cohort.Communications biology · 2026Article
- Assessment of long-read strategies for the enrichment of clinically relevant breakpoints in lymphomas: towards a diagnostic implementation.Annals of hematology · 2026Article
Corrections and comments
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Authors and funding
2 authors.
Funding
Abstract
Short- and long-read sequencing technologies are routinely used to detect DNA variants, including SNVs, indels, and structural variations (SVs). However, the differences in the quality and quantity of variants detected between short- and long-read data are not fully understood. In this study, we comprehensively evaluated the variant calling performance of short- and long-read-based SNV, indel, and SV detection algorithms (6 for SNVs, 12 for indels, and 13 for SVs) using a novel evaluation framework incorporating manual visual inspection. The results showed that indel-insertion calls greater than 10 bp were poorly detected by short-read-based detection algorithms compared to long-read-based algorithms; however, the recall and precision of SNV and indel-deletion detection were similar between short- and long-read data. The recall of SV detection with short-read-based algorithms was significantly lower in repetitive regions, especially for small- to intermediate-sized SVs, than that detected with long-read-based algorithms. In contrast, the recall and precision of SV detection in nonrepetitive regions were similar between short- and long-read data. These findings suggest the need for refined strategies, such as incorporating multiple variant detection algorithms, to generate a more complete set of variants using short-read 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.