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Acceleration of Variant Discovery Tool in GATK
2018 IEEE 23rd International Conference on Digital Signal Processing (DSP), 2018This work presents a digital hardware design to accelerate the HaplotypeCaller in the Variant Discovery phase of Genome Analysis Tool-Kit (GATK), which is a software toolkit for genetic sequencing data analyzing. We implement and redesign HaplotypeCaller by using a software-hardware co-design environment composed of C++ and Verilog, and program the ...
Sao-Jie Chen
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Evaluation of an optimized germline exomes pipeline using BWA-MEM2 and Dragen-GATK tools
PLoS ONE, 2023 The next-generation sequencing (NGS) technology represents a significant advance in genomics and medical diagnosis. Nevertheless, the time it takes to perform sequencing, data analysis, and variant interpretation is a bottleneck in using next-generation sequencing in precision medicine.
Nofe Alganmi
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Investigating Genome Analysis Pipeline Performance on GATK with Cloud Object Storage
2020 28th International Symposium on Modeling, Analysis, and Simulation of Computer and Telecommunication Systems (MASCOTS), 2020Achieving fast, scalable, and cost-effective genome analytics is always important to open up a new frontier in biomedical and life science. Genome Analysis Toolkit (GATK), an industry-standard genome analysis tool, improves its scalability and performance by leveraging Spark and HDFS.
Tatsuhiro Chiba
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GATK hard filtering: tunable parameters to improve variant calling for next generation sequencing targeted gene panel data [PDF]
BMC Bioinformatics, 2017 BACKGROUND: NGS technology represents a powerful alternative to the standard Sanger sequencing in the context of clinical setting. The proprietary software that are generally used for variant calling often depend on preset parameters that may not fit in
Giovanni Malerba +2 more
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GATK-gCNV enables the discovery of rare copy number variants from exome sequencing data
Nature Genetics, 2023Copy number variants (CNVs) are major contributors to genetic diversity and disease. While standardized methods, such as the genome analysis toolkit (GATK), exist for detecting short variants, technical challenges have confounded uniform large-scale CNV analyses from whole-exome sequencing (WES) data.
Mark A Walker +2 more
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GPU-Accelerated GATK HaplotypeCaller with Load-Balanced Multi-Process Optimization
2017 IEEE 17th International Conference on Bioinformatics and Bioengineering (BIBE), 2017Due to its high-throughput and low cost, Next Generation Sequencing (NGS) technology is becoming increasingly popular in many genomics research labs. However, handling the massive raw data generated by the NGS platforms poses a significant computational challenge to genomics analysis tools.
Zaid Al-Ars, Koen Bertels
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Advances in Intelligent and Soft Computing, 2011
Bisulfite sequencing is a technique that can be combined with next-generation sequencing approaches to analyze DNA methylation patterns in a genome wide scale. The GATK framework is a new Java framework for fast-developing NGS applications including capabilities for automatic shared-memory parallelization.
Florentino Fdez-Riverola +2 more
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Bisulfite sequencing is a technique that can be combined with next-generation sequencing approaches to analyze DNA methylation patterns in a genome wide scale. The GATK framework is a new Java framework for fast-developing NGS applications including capabilities for automatic shared-memory parallelization.
Florentino Fdez-Riverola +2 more
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Cluster-based Apache Spark implementation of the GATK DNA analysis pipeline
2015 IEEE International Conference on Bioinformatics and Biomedicine (BIBM), 2015Fast progress in next generation sequencing has dramatically increased the throughout of DNA sequencing, resulting in the availability of large DNA data sets ready for analysis. However, post-sequencing DNA analysis has become the bottleneck in using these data sets, as it requires powerful and scalable tools to perform the needed analysis.
Zaid Al-Ars, Hamid Mushtaq
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GATK PathSeq: a customizable computational tool for the discovery and identification of microbial sequences in libraries from eukaryotic hosts. [PDF]
Bioinformatics, 2018 Abstract Summary We present an updated version of our computational pipeline, PathSeq, for the discovery and identification of microbial sequences in genomic and transcriptomic libraries from eukaryotic hosts.
Mark A Walker +2 more
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Abstract 2287: Precise common and rare germline CNV calling with GATK
Cancer Research, 2018Abstract We propose, implement, and evaluate a novel method (GATK gCNV) for accurate discovery of rare and common copy-number variations (CNVs) from read-depth data obtained from whole genome sequencing (WGS), whole exome sequencing (WES), or custom gene panels.
Mehrtash Babadi +6 more
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