ArticleBMC genomics2020
GSAlign: an efficient sequence alignment tool for intra-species genomes.
Article in BMC genomics, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 30 papers.
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Who cites it
30 citing papers in PubMed.
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- Accelerating minimap2 for whole-genome alignment.Bioinformatics (Oxford, England) · 2026Article
- Transposable elements as drivers of genome evolution in Drosophila virilis.Nucleic acids research · 2026Article
- RLBWT-Based LCP Computation in Compressed Space for Terabase-Scale Pangenome Analysis.bioRxiv : the preprint server for biology · 2026Article
- AlloSHP: deconvoluting single homeologous polymorphism for phylogenetic analysis of allopolyploids.Plant methods · 2025Article
- Accurate, Scalable Structural Variant Genotyping in Complex Genomes at Population Scales.Molecular biology and evolution · 2025Article
- Pangenome graph mitigates heterozygosity overestimation from mapping bias: a case study in Chinese indigenous pigs.BMC biology · 2025Article
- Benchmarking, detection, and genotyping of structural variants in a population of whole-genome assemblies using the SVGAP pipeline.bioRxiv : the preprint server for biology · 2025Article
- Characteristics and filtering of low-frequency artificial short deletion variations based on nanopore sequencing.GigaScience · 2025Article
- Sequencing of the chloroplast genome of Taimo, a paddy cultivar of Taro (Mitochondrial DNA. Part B, Resources · 2025Article
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- Telomere-to-telomere genome assembly of the aflatoxin biocontrol agentMicrobiology resource announcements · 2024Article
- Construction of Streptomyces coelicolor A3(2) mutants that exclusively produce NA4/NA6 intermediates of agarose metabolism through mutation induction.Scientific reports · 2023Article
- CoreDetector: a flexible and efficient program for core-genome alignment of evolutionary diverse genomes.Bioinformatics (Oxford, England) · 2023Article
- GET_PANGENES: calling pangenes from plant genome alignments confirms presence-absence variation.Genome biology · 2023Article
- Complete genome of the toxic mold Aspergillus pseudotamarii isolate NRRL 25517 reveals genomic instability of the aflatoxin biosynthesis cluster.G3 (Bethesda, Md.) · 2023Article
- Article
- Long-read-based draft genome sequence of Indian black gram IPU-94-1 'Uttara': Insights into disease resistance and seed storage protein genes.The plant genome · 2022Article
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2 authors.
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Abstract
backgroundPersonal genomics and comparative genomics are becoming more important in clinical practice and genome research. Both fields require sequence alignment to discover sequence conservation and variation. Though many methods have been developed, some are designed for small genome comparison while some are not efficient for large genome comparison. Moreover, most existing genome comparison tools have not been evaluated the correctness of sequence alignments systematically. A wrong sequence alignment would produce false sequence variants.
resultsIn this study, we present GSAlign that handles large genome sequence alignment efficiently and identifies sequence variants from the alignment result. GSAlign is an efficient sequence alignment tool for intra-species genomes. It identifies sequence variations from the sequence alignments. We estimate performance by measuring the correctness of predicted sequence variations. The experiment results demonstrated that GSAlign is not only faster than most existing state-of-the-art methods, but also identifies sequence variants with high accuracy.
conclusionsAs more genome sequences become available, the demand for genome comparison is increasing. Therefore an efficient and robust algorithm is most desirable. We believe GSAlign can be a useful tool. It exhibits the abilities of ultra-fast alignment as well as high accuracy and sensitivity for detecting sequence variations.
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