Results 1 to 10 of about 74,514 (109)

Benchmarking of variant calling software for whole-exome sequencing using gold standard datasets [PDF]

Scientific Reports
Accurate variant calling from whole-exome sequencing (WES) data is vital for understanding genetic diseases. Recently, commercial variant calling software have emerged that do not require bioinformatics or programming expertise, hence enabling ...
Matthew Wong, Bryan Liew, Melissa Hum, Ning Yuan Lee, Ann S. G. Lee   +4 more
doaj   +3 more sources

Artificial intelligence in variant calling: a review [PDF]

Frontiers in Bioinformatics
Artificial intelligence (AI) has revolutionized numerous fields, including genomics, where it has significantly impacted variant calling, a crucial process in genomic analysis.
Omar Abdelwahab, Omar Abdelwahab, Omar Abdelwahab, Omar Abdelwahab, Davoud Torkamaneh, Davoud Torkamaneh, Davoud Torkamaneh, Davoud Torkamaneh   +7 more
doaj   +4 more sources

Variant calling in polyploids for population and quantitative genetics [PDF]

Applications in Plant Sciences
Advancements in genome assembly and sequencing technology have made whole genome sequence (WGS) data and reference genomes accessible to study polyploid species.
Alyssa R. Phillips
doaj   +3 more sources

Aggregate variant calling using short reads enables population and disease studies for paralogous genes [PDF]

HGG Advances
Summary: Variant calling in paralogous genes using short-read sequencing is problematic due to mapping ambiguity between highly similar sequences. Aggregate variant calling, which treats paralogous loci as a single locus by realigning reads to a masked ...
Timofey Prodanov, Sang Yoon Byun, Vikas Bansal   +2 more
doaj   +2 more sources

Calling Variants in the Clinic: Informed Variant Calling Decisions Based on Biological, Clinical, and Laboratory Variables

Computational and Structural Biotechnology Journal, 2019
Deep sequencing genomic analysis is becoming increasingly common in clinical research and practice, enabling accurate identification of diagnostic, prognostic, and predictive determinants.
Zachary S. Bohannan, Antonina Mitrofanova   +1 more
doaj   +3 more sources

A review of somatic single nucleotide variant calling algorithms for next-generation sequencing data

Computational and Structural Biotechnology Journal, 2018
Detection of somatic mutations holds great potential in cancer treatment and has been a very active research field in the past few years, especially since the breakthrough of the next-generation sequencing technology.
Chang Xu
doaj   +3 more sources

Benchmarking datasets for assembly-based variant calling using high-fidelity long reads

BMC Genomics, 2023
Background Recent advances in long-read sequencing technologies have enabled accurate identification of all genetic variants in individuals or cells; this procedure is known as variant calling.
Hyunji Lee, Jun Kim, Junho Lee
doaj   +1 more source

Tool evaluation for the detection of variably sized indels from next generation whole genome and targeted sequencing data.

PLoS Computational Biology, 2022
Insertions and deletions (indels) in human genomes are associated with a wide range of phenotypes, including various clinical disorders. High-throughput, next generation sequencing (NGS) technologies enable the detection of short genetic variants, such ...
Ning Wang, Vladislav Lysenkov, Katri Orte, Veli Kairisto, Juhani Aakko, Sofia Khan, Laura L Elo   +6 more
doaj   +1 more source

OVarFlow: a resource optimized GATK 4 based Open source Variant calling workFlow

BMC Bioinformatics, 2021
Background The advent of next generation sequencing has opened new avenues for basic and applied research. One application is the discovery of sequence variants causative of a phenotypic trait or a disease pathology.
Jochen Bathke, Gesine Lühken
doaj   +1 more source

vcfdist: accurately benchmarking phased small variant calls in human genomes

Nature Communications, 2023
Accurately benchmarking small variant calling accuracy is critical for the continued improvement of human whole genome sequencing. In this work, we show that current variant calling evaluations are biased towards certain variant representations and may ...
Tim Dunn, Satish Narayanasamy
doaj   +1 more source