Results 31 to 40 of about 709,139 (287)

ICR142 Benchmarker: evaluating, optimising and benchmarking variant calling performance using the ICR142 NGS validation series [version 2; referees: 2 approved]

Wellcome Open Research, 2018
Evaluating, optimising and benchmarking of next generation sequencing (NGS) variant calling performance are essential requirements for clinical, commercial and academic NGS pipelines.
Elise Ruark, Esty Holt, Anthony Renwick, Márton Münz, Matthew Wakeling, Sian Ellard, Shazia Mahamdallie, Shawn Yost, Nazneen Rahman   +8 more
doaj   +1 more source

Performance analysis of conventional and AI-based variant callers using short and long reads

BMC Bioinformatics, 2023
Background The accurate detection of variants is essential for genomics-based studies. Currently, there are various tools designed to detect genomic variants, however, it has always been a challenge to decide which tool to use, especially when various ...
Omar Abdelwahab, François Belzile, Davoud Torkamaneh   +2 more
doaj   +1 more source

Inexpensive and Highly Reproducible Cloud-Based Variant Calling of 2,535 Human Genomes. [PDF]

PLoS ONE, 2015
Population scale sequencing of whole human genomes is becoming economically feasible; however, data management and analysis remains a formidable challenge for many research groups.
Suyash S Shringarpure, Andrew Carroll, Francisco M De La Vega, Carlos D Bustamante   +3 more
doaj   +1 more source

Variant calling filters.

, 2021
List of filtering criteria used during somatic variant calling. (XLSX)
Lilja Jansson (9620924), Miko Valori (5865947), Pentti J. Tienari (9620939)   +2 more
core   +1 more source

Sentieon DNASeq Variant Calling Workflow Demonstrates Strong Computational Performance and Accuracy

Frontiers in Genetics, 2019
As reliable, efficient genome sequencing becomes ubiquitous, the need for similarly reliable and efficient variant calling becomes increasingly important.
Katherine I. Kendig, Saurabh Baheti, Matthew A. Bockol, Travis M. Drucker, Steven N. Hart, Jacob R. Heldenbrand, Mikel Hernaez, Matthew E. Hudson, Matthew E. Hudson, Michael T. Kalmbach, Eric W. Klee, Nathan R. Mattson, Christian A. Ross, Morgan Taschuk, Eric D. Wieben, Mathieu Wiepert, Derek E. Wildman, Derek E. Wildman, Liudmila S. Mainzer, Liudmila S. Mainzer   +19 more
doaj   +1 more source

ToTem: a tool for variant calling pipeline optimization [PDF]

BMC Bioinformatics, 2018
High-throughput bioinformatics analyses of next generation sequencing (NGS) data often require challenging pipeline optimization. The key problem is choosing appropriate tools and selecting the best parameters for optimal precision and recall.Here we introduce ToTem, a tool for automated pipeline optimization.
Nikola Tom, Ondrej Tom, Jitka Malcikova, Sarka Pavlova, Blanka Kubesova, Tobias Rausch, Miroslav Kolarík, Vladimir Benes, Vojtech Bystrý, Sarka Pospisilova   +9 more
openaire   +3 more sources

HaploTypo: a variant-calling pipeline for phased genomes [PDF]

Bioinformatics, 2019
Abstract Summary An increasing number of phased (i.e. with resolved haplotypes) reference genomes are available. However, the most genetic variant calling tools do not explicitly account for haplotype structure. Here, we present HaploTypo, a pipeline tailored to resolve haplotypes in genetic variation
Cinta Pegueroles, Verónica Mixão, Laia Carreté, Manuel Molina, Toni Gabaldón   +4 more
openaire   +4 more sources

Best Practices for Evaluating Single Nucleotide Variant Calling Methods for Microbial Genomics

Frontiers in Genetics, 2015
Innovations in sequencing technologies have allowed biologists to make incredible advances in understanding biological systems. As experience grows, researchers increasingly recognize that analyzing the wealth of data provided by these new sequencing ...
Nathan eOlson, Steven P. Lund, Rebecca E. Colman, Jeffrey T Foster, Jason W Sahl, James M Schupp, Paul eKeim, Paul eKeim, Jayne B Morrow, Marc L Salit, Marc L Salit, Justin M Zook   +11 more
doaj   +1 more source

Evaluation of variant calling tools for large plant genome re-sequencing

BMC Bioinformatics, 2020
Background Discovering single nucleotide polymorphisms (SNPs) from agriculture crop genome sequences has been a widely used strategy for developing genetic markers for several applications including marker-assisted breeding, population diversity studies ...
Zhen Yao, Frank M. You, Amidou N’Diaye, Ron E. Knox, Curt McCartney, Colin W. Hiebert, Curtis Pozniak, Wayne Xu   +7 more
doaj   +1 more source

Snpeff variant calling results.

, 2023
T. trichiura China (GU385218) is used as reference genome for variant calling since it is the closest published reference mitogenome. (DOCX)
Min-Ho Choi (112334), Yuan Yi Chang (16892374), Hyun Beom Song (644078), Heekyoung Kang (2186341), Jun Kim (238502), James Owen Delaluna (16892371), MinJi Kim (16892377)   +6 more
core   +1 more source