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  1. Article

    Open Access

    A draft human pangenome reference

    Here the Human Pangenome Reference Consortium presents a first draft of the human pangenome reference. The pangenome contains 47 phased, diploid assemblies from a cohort of genetically diverse individuals1. These...

    Wen-Wei Liao, Mobin Asri, Jana Ebler, Daniel Doerr, Marina Haukness, Glenn Hickey… in Nature (2023)

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  2. No Access

    Article

    DeepConsensus improves the accuracy of sequences with a gap-aware sequence transformer

    Circular consensus sequencing with Pacific Biosciences (PacBio) technology generates long (10–25 kilobases), accurate ‘HiFi’ reads by combining serial observations of a DNA molecule into a consensus sequence. ...

    Gunjan Baid, Daniel E. Cook, Kishwar Shafin, Taedong Yun… in Nature Biotechnology (2023)

  3. Article

    Open Access

    Accelerated identification of disease-causing variants with ultra-rapid nanopore genome sequencing

    Whole-genome sequencing (WGS) can identify variants that cause genetic disease, but the time required for sequencing and analysis has been a barrier to its use in acutely ill patients. In the present study, we...

    Sneha D. Goenka, John E. Gorzynski, Kishwar Shafin, Dianna G. Fisk… in Nature Biotechnology (2022)

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    Article

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

    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-gener...

    Kishwar Shafin, Trevor Pesout, Pi-Chuan Chang, Maria Nattestad… in Nature Methods (2021)

  5. Article

    Open Access

    BigTop: a three-dimensional virtual reality tool for GWAS visualization

    Genome-wide association studies (GWAS) are typically visualized using a two-dimensional Manhattan plot, displaying chromosomal location of SNPs along the x-axis and the negative log-10 of their p-value on the y-a...

    Samuel T. Westreich, Maria Nattestad, Christopher Meyer in BMC Bioinformatics (2020)

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  6. No Access

    Article

    Accurate detection of complex structural variations using single-molecule sequencing

    Structural variations are the greatest source of genetic variation, but they remain poorly understood because of technological limitations. Single-molecule long-read sequencing has the potential to dramaticall...

    Fritz J. Sedlazeck, Philipp Rescheneder, Moritz Smolka, Han Fang… in Nature Methods (2018)

  7. No Access

    Article

    Phased diploid genome assembly with single-molecule real-time sequencing

    The open-source FALCON and FALCON-Unzip software utilize long-read sequencing data to generate contiguous, accurate and phased diploid assemblies, even from genomes that are highly heterozygous.

    Chen-Shan Chin, Paul Peluso, Fritz J Sedlazeck, Maria Nattestad… in Nature Methods (2016)