Article

Joint processing of long- and short-read sequencing data with deep learning improves variant calling

2024-12-02

Abstract excerpt

<h4>ABSTRACT</h4> Despite the complementary strengths of short- and long-read sequencing approaches, variant calling methods still rely on a single data type. In this study, we collected and harmonized Nanopore dataset of the 7 GIAB healthy individuals across three independent consortia. Then, by leveraging these harmonized Nanopore data, we explore the benefits of using a hybrid DeepVariant model to jointly proc...

Topics

Open a Topic to create a Post that cites this publication.

Identifiers and source

Literature Corpus work: e4a24f85-c19b-52b0-8c83-2487cd6756e9
DOI: 10.1101/2024.11.26.625492

Open publication

Related research

Semantic proximity does not establish scientific evidence.

Click a neighbor to travelStep 1 · 12 closest

Joint processing of long- and short-read sequencing data with deep learning improves variant callingDOI 10.1101/2024.11.26.625492Read

Finding an optimal sequencing strategy to detect short and long genetic variants in a human genomeSemantic proximity Read

Benchmarking of sequencing technologies defines optimal strategies for genetic variants detection in a human genome.Semantic proximity Read

Investigating the performance of Oxford Nanopore long-read sequencing with respect to Illumina microarrays and short-read sequencingSemantic proximity Read

Accelerated and High-Accuracy Variant Calling on Oxford Nanopore Technologies Sequencing Data with the Sentieon DNAscope LongRead and Hybrid PipelinesSemantic proximity Read

Accelerated, Accurate, Hybrid Short and Long Reads Alignment and Variant CallingSemantic proximity Read

Whole-genome long-read sequencing downsampling and its effect on variant calling precision and recallSemantic proximity Read

Evaluation of the Available Variant Calling Tools for Oxford Nanopore Sequencing in Breast Cancer.Semantic proximity Read

DeepSomatic: Accurate somatic small variant discovery for multiple sequencing technologiesSemantic proximity Read

HiFi long-read genomes for difficult-to-detect clinically relevant variantsSemantic proximity Read

miniSNV: accurate and fast single nucleotide variant calling from nanopore sequencing data.Semantic proximity Read

Benchmarking small variant detection with ONT reveals high performance in challenging regionsSemantic proximity Read

Long-range PCR and Nanopore sequencing for localisation and phasing variants: an end-to-end clinical application workflowSemantic proximity Read