Haplotype-aware variant calling with PEPPER-Margin-DeepVariant enables high accuracy in nanopore long-reads

• Published in: Nature methods Vol. 18; no. 11; pp. 1322 - 1332
• Main Authors: Shafin, Kishwar, Pesout, Trevor, Chang, Pi-Chuan, Nattestad, Maria, Kolesnikov, Alexey, Goel, Sidharth, Baid, Gunjan, Kolmogorov, Mikhail, Eizenga, Jordan M., Miga, Karen H., Carnevali, Paolo, Jain, Miten, Carroll, Andrew, Paten, Benedict
• Format: Journal Article
• Language: English
• Published: New York Nature Publishing Group US 01.11.2021; Nature Publishing Group
• Subjects: 631/114/1305; 631/114/2785; 631/1647/794; 631/208/726/649; 631/61/212; Bioinformatics; Biological Microscopy; Biological Techniques; Biomedical and Life Sciences; Biomedical Engineering/Biotechnology; Diploids; DNA sequencing; Genes; Genetic research; Genetic variation; Genome, Human; Genomes; Genomics; Genotyping; Haplotypes; High-Throughput Nucleotide Sequencing - methods; Humans; Identification methods; Life Sciences; Methods; Molecular Sequence Annotation; Nanopores; Nanotechnology; Nucleotide sequencing; Nucleotides; Pipelines; Polymorphism, Single Nucleotide; Proteomics; Sequence Analysis, DNA - methods; Software; Vegetables; United States

Long-read sequencing has the potential to transform variant detection by reaching currently difficult-to-map regions and routinely linking together adjacent variations to enable read-based phasing. Third-generation nanopore sequence data have demonstrated a long read length, but current interpretati...