Results 11 to 20 of about 37,179 (261)
GPU accelerated sequence alignment with traceback for GATK HaplotypeCaller [PDF]
BMC Genomics, 2019 Background Pairwise sequence alignment is widely used in many biological tools and applications. Existing GPU accelerated implementations mainly focus on calculating optimal alignment score and omit identifying the optimal alignment itself.
Shanshan Ren +3 more
doaj +7 more sources
OVarFlow: a resource optimized GATK 4 based Open source Variant calling workFlow [PDF]
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 +8 more sources
BMC BiologyBackground Single-nucleotide polymorphisms (SNPs) are the most widely used form of molecular genetic variation studies. As reference genomes and resequencing data sets expand exponentially, tools must be in place to call SNPs at a similar pace.
Yong Zhou +18 more
doaj +6 more sources
Design and evaluation of a genomics variant analysis pipeline using GATK Spark tools
CoRR, 2018 Scalable and efficient processing of genome sequence data, i.e. for variant discovery, is key to the mainstream adoption of High Throughput technology for disease prevention and for clinical use. Achieving scalability, however, requires a significant effort to enable the parallel execution of the analysis tools that make up the pipelines.
Nicholas Tucci +3 more
core +13 more sources
Acceleration of the Pair-HMM forward algorithm on FPGA with cloud integration for GATK [PDF]
2019 IEEE International Conference on Bioinformatics and Biomedicine (BIBM), 2019 The Pair-HMM forward algorithm is an essential algorithm found in many genomic related analyses. The high number of floating point operations in the algorithm makes it one of the main contributors to the compute time of analysis pipelines. To speed-up computations we propose an FPGA-based hardware accelerator for the Amazon AWS F1 Cloud platform.
Rick Wertenbroek, Yann Thoma
openaire +2 more sources
Expanding guitar production techniques : building the guitar application toolkit (GATK) [PDF]
, 2017 The purpose of this thesis was to build the Guitar Application ToolKit (GATK), a series of applications used to expand the sonic capabilities of the acoustic/electric stereo guitar.
Aramburu, Roberto Horacio
openaire +3 more sources
The GATK joint genotyping workflow is appropriate for calling variants in RNA-seq experiments [PDF]
Journal of Animal Science and Biotechnology, 2019 The Genome Analysis Toolkit (GATK) is a popular set of programs for discovering and genotyping variants from next-generation sequencing data. The current GATK recommendation for RNA sequencing (RNA-seq) is to perform variant calling from individual ...
Jean-Simon Brouard +3 more
doaj +3 more sources
Optimizing performance of GATK workflows using Apache Arrow In-Memory data framework [PDF]
BMC Genomics, 2020 Background Immense improvements in sequencing technologies enable producing large amounts of high throughput and cost effective next-generation sequencing (NGS) data. This data needs to be processed efficiently for further downstream analyses.
Tanveer Ahmad +3 more
doaj +5 more sources
Abstract 3581: GATK ACNV: allelic copy-number variation discovery from SNPs and coverage data
Cancer Research, 2017 Abstract The presence of somatic copy-number alterations in tumor genomes can be used to predict both patient sensitivity to treatments as well as outcomes. The inclusion of allelic data improves statistical power to detect copy-number events and allows for discovery of copy-neutral events.
Aaron Chevalier +6 more
openaire +2 more sources