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Quality Metrics for Benchmarking Sequences Comparison Tools [chapter]

Erwan Drezen, Dominique Lavenier
2014 Lecture Notes in Computer Science  
Results: A set of quality metrics is proposed that enables a systematic approach for comparing alignment tools.  ...  These metrics have been implemented in a dedicated software, allowing to produce textual and graphical benchmark artifacts.  ...  The trade-off between speed and quality is the key point. As a consequence, to evaluate new Alignement Search Tools (AST for short), benchmarking has to focus on time and quality metrics.  ... 
doi:10.1007/978-3-319-12418-6_18 fatcat:dy2bifg63barfk7mrjd53helbq

SeqPurge: highly-sensitive adapter trimming for paired-end NGS data

Marc Sturm, Christopher Schroeder, Peter Bauer
2016 BMC Bioinformatics  
The very good adapter trimming performance, complemented with additional features such as quality-based trimming and basic quality control, makes SeqPurge an excellent choice for the pre-processing of  ...  However, our evaluation on amplicon-based data shows that most of the current tools are not able to remove all adapter sequences and that adapter contamination may even lead to spurious variant calls.  ...  The adapter trimming benchmarks presented so far, did not take trimming of low-quality bases into account. We excluded this feature, because not all tools in the comparison support it.  ... 
doi:10.1186/s12859-016-1069-7 pmid:27161244 pmcid:PMC4862148 fatcat:6asqtwyky5gz5mfrxdqoqcdn5a

An analytical framework for optimizing variant discovery from personal genomes

Gareth Highnam, Jason J. Wang, Dean Kusler, Justin Zook, Vinaya Vijayan, Nir Leibovich, David Mittelman
2015 Nature Communications  
Here we present the genome comparison and analytic testing (GCAT) platform to facilitate development of performance metrics and comparisons of analysis tools across these metrics.  ...  Performance is reported through interactive visualizations of benchmark and performance testing data, with support for data slicing and filtering.  ...  Acknowledgements We would like to thank Dr Gholson Lyon and Gabe Rudy for critical feedback and suggestions throughout the development of the project.  ... 
doi:10.1038/ncomms7275 pmid:25711446 pmcid:PMC4351570 fatcat:wkggp3ebg5fjpkq3fbfjxqwdlq

Set-theory based benchmarking of three different variant callers for targeted sequencing

Jose Arturo Molina-Mora, Mariela Solano-Vargas
2021 BMC Bioinformatics  
Performance metrics using our set-theory approach showed high-resolution pipelines and revealed: (1) a perfect recall of 1.000 for all three pipelines, (2) very high precision values, i.e. 0.987 for Freebayes  ...  According to the benchmarking framework of the Global Alliance for Genomics and Health (GA4GH), we implemented a new simple and user-friendly set-theory based method to assess variant callers using a gold  ...  Mariángela Vargas Arroyo Ph.D. for the critical comments of this paper.  ... 
doi:10.1186/s12859-020-03926-3 pmid:33413082 fatcat:s4aj7tjcurdnxjq5xn4bcnfg44

GenomeQC: A quality assessment tool for genome assemblies and gene structure annotations [article]

Nancy Manchanda, John L Portwood, Margaret R Woodhouse, Arun Seetharam, Carolyn J Lawrence-Dill, Carson M Andorf, Matthew Hufford
2019 bioRxiv   pre-print
Here, we describe a new toolkit that integrates multiple metrics to characterize both assembly and gene annotation quality in a way that enables comparison across multiple assemblies and assembly types  ...  While several tools exist for calculating individual metrics, applications providing comprehensive evaluations of multiple assembly features are, perhaps surprisingly, lacking.  ...  Acknowledgements The authors would like to thank Levi Baber (Iowa State University Director of Research IT) for technical help and Jack Gardiner (Curator at MaizeGDB) for testing the web application and  ... 
doi:10.1101/795237 fatcat:ikp2wizqbrb35fbd3ph7afcyjy

Best practices for benchmarking germline small-variant calls in human genomes

Peter Krusche, Len Trigg, Paul C. Boutros, Christopher E. Mason, Francisco M. De La Vega, Benjamin L. Moore, Mar Gonzalez-Porta, Michael A. Eberle, Zivana Tezak, Samir Lababidi, Rebecca Truty, George Asimenos (+5 others)
2019 Nature Biotechnology  
Standardized benchmarking approaches are required to assess the accuracy of variants called from sequence data.  ...  Here, as part of the Global Alliance for Genomics and Health (GA4GH), we present a benchmarking framework for variant calling.  ...  Acknowledgments We thank GA4GH, especially Stephen Keenan, David Lloyd, and Rishi Nag, for their support in hosting and organizing the Benchmarking Team.  ... 
doi:10.1038/s41587-019-0054-x pmid:30858580 pmcid:PMC6699627 fatcat:oggljypeprcihpczqvqhqifpci

Best Practices for Benchmarking Germline Small Variant Calls in Human Genomes [article]

Peter Krusche, Len Trigg, Paul C Boutros, Christopher E Mason, Francisco M De La Vega, Benjamin L Moore, Mar Gonzalez-Porta, Michael A Eberle, Zivana Tezak, Samir Labadibi, Rebecca Truty, George Asimenos (+5 others)
2018 bioRxiv   pre-print
Benchmarking variant calls requires careful attention to definitions of performance metrics, sophisticated comparison approaches, and stratification by variant type and genome context.  ...  To address these needs, the Global Alliance for Genomics and Health (GA4GH) Benchmarking Team convened representatives from sequencing technology developers, government agencies, academic bioinformatics  ...  Acknowledgments We thank GA4GH, especially Stephen Keenan, David Lloyd, and Rishi Nag, for their support in hosting and organizing the Benchmarking Team.  ... 
doi:10.1101/270157 fatcat:ainuuuc4rvebpkk2hcj4iimium

Appendix [chapter]

Shahriar Akramullah
2014 Digital Video Concepts, Methods, and Metrics  
The PSNR, SSIM, and MS-SSIM were used as the comparison objective metrics on all the color planes Y, U, and V for all frames in the video sequences.  ...  PCMark and PowerMark These benchmarks were developed by FutureMark. PCMark is a standard performance benchmarking tool for personal computers of various form factors.  ... 
doi:10.1007/978-1-4302-6713-3_10 fatcat:xtznaxwsbrhonmyz5x6gt4zb5y

Normalized Workflow to Optimize Hybrid De Novo Transcriptome Assembly for Non-Model Species: A Case Study in Lilium ledebourii (Baker) Boiss

Morteza Sheikh-Assadi, Roohangiz Naderi, Seyed Alireza Salami, Mohsen Kafi, Reza Fatahi, Vahid Shariati, Federico Martinelli, Angela Cicatelli, Maria Triassi, Francesco Guarino, Giovanni Improta, Manuel Gonzalo Claros
2022 Plants  
Nevertheless, the effectuality of tools for de novo assembly and real precision assembled transcriptomes looks somewhat unexplored, particularly for non-model organisms with complicated (very long, heterozygous  ...  A high-quality transcriptome is required to advance numerous bioinformatics workflows.  ...  Workflow of cDNA library construction, RNA-sequencing, and de novo transcriptome analysis and benchmarking. 1 1 Figure 2 . 2 Figure 2. The quality assessment results for the trimmed RNA-Seq data.  ... 
doi:10.3390/plants11182365 pmid:36145766 fatcat:s55vxfkxzfdy3me6vtytijwpki

RNA-Puzzles toolkit: a computational resource of RNA 3D structure benchmark datasets, structure manipulation, and evaluation tools

2019 Nucleic Acids Research  
3D structure normalization, analysis, manipulation, visualization tools (RNA_format, RNA_normalizer, rna-tools) and (iii) 3D structure comparison metric tools (RNAQUA, MCQ4Structures).  ...  The RNA-Puzzles contest has shown, among others, that the development and validation of computational methods for RNA fold prediction strongly depend on the benchmark datasets and the structure comparison  ...  tools, (iii) and 3D structure comparison metrics ( Figure 1 ).  ... 
doi:10.1093/nar/gkz1108 pmid:31799609 pmcid:PMC7145511 fatcat:aua3ozugyzdzxoylcobu6fle7u

GenomeQC: a quality assessment tool for genome assemblies and gene structure annotations

Nancy Manchanda, John L. Portwood, Margaret R. Woodhouse, Arun S. Seetharam, Carolyn J. Lawrence-Dill, Carson M. Andorf, Matthew B. Hufford
2020 BMC Genomics  
Here, we describe a new toolkit that integrates multiple metrics to characterize both assembly and gene annotation quality in a way that enables comparison across multiple assemblies and assembly types  ...  While several tools exist for calculating individual metrics, applications providing comprehensive evaluations of multiple assembly features are, perhaps surprisingly, lacking.  ...  Acknowledgements The authors would like to thank Levi Baber (Iowa State University Director of Research IT) for technical help and Jack Gardiner (Curator at MaizeGDB) for testing the web application and  ... 
doi:10.1186/s12864-020-6568-2 pmid:32122303 pmcid:PMC7053122 fatcat:pzdtu77o5rgmlnxozqx7xgrsiy

FDA-ARGOS is a database with public quality-controlled reference genomes for diagnostic use and regulatory science

Heike Sichtig, Timothy Minogue, Yi Yan, Christopher Stefan, Adrienne Hall, Luke Tallon, Lisa Sadzewicz, Suvarna Nadendla, William Klimke, Eneida Hatcher, Martin Shumway, Dayanara Lebron Aldea (+6 others)
2019 Nature Communications  
We provide quality control metrics for the FDA-ARGOS genomic database resource and outline the need for genome quality gap filling in the public domain.  ...  In the second use case, we demonstrate the utility of FDA-ARGOS reference genomes for Ebola virus target sequence comparison as part of a composite validation strategy for ID-NGS diagnostic tests.  ...  This table shows the traditional benchmark comparison of the EBOV MIPS assay to real-time PCR (RT-PCR) results and target sequence comparison with FDA-ARGOS using three bioinformatics tools (MegaBLAST,  ... 
doi:10.1038/s41467-019-11306-6 pmid:31346170 pmcid:PMC6658474 fatcat:ek46vv5u6rghbbt6rpfhr2vuei

How to benchmark objective quality metrics from paired comparison data?

Philippe Hanhart, Lukas Krasula, Patrick Le Callet, Touradj Ebrahimi
2016 2016 Eighth International Conference on Quality of Multimedia Experience (QoMEX)  
The procedures commonly used to evaluate the performance of objective quality metrics rely on ground truth mean opinion scores and associated confidence intervals, which are usually obtained via direct  ...  This tool can be used to further assess the performance of objective metrics based on ground truth preference scores.  ...  These tools enable to directly use the results obtained in PC experiments for the benchmarking of objective metrics.  ... 
doi:10.1109/qomex.2016.7498960 dblp:conf/qomex/HanhartKCE16 fatcat:cqce5nbhsbc4pcfceovnmeno4m

iCOMIC: a graphical interface-driven bioinformatics pipeline for analyzing cancer omics data [article]

Anjana Anilkumar Sithara, Devi Priyanka Maripuri, Keerthika Moorthy, Sai Sruthi Amirtha Ganesh, Philge Philip, Shayantan Banerjee, Malvika Sudhakar, Karthik Raman
2021 bioRxiv   pre-print
We benchmarked our tool against Genome In A Bottle (GIAB) benchmark dataset (NA12878) and got the highest F1 score of 0.971 and 0.988 for indels and SNPs, respectively, using the BWA MEM - GATK HC DNA-Seq  ...  Despite the tremendous increase in omics data generated by modern sequencing technologies, their analysis can be tricky and often requires substantial expertise in bioinformatics.  ...  Acknowledgements The authors acknowledge Mr Likith Reddy for preliminary benchmarking studies and other members of the lab for useful discussions.  ... 
doi:10.1101/2021.09.18.460896 fatcat:yxn7tzf5xjbxlo4mb4vsudlluy

Best practices for evaluating single nucleotide variant calling methods for microbial genomics

Nathan D. Olson, Steven P. Lund, Rebecca E. Colman, Jeffrey T. Foster, Jason W. Sahl, James M. Schupp, Paul Keim, Jayne B. Morrow, Marc L. Salit, Justin M. Zook
2015 Frontiers in Genetics  
As experience grows, researchers increasingly recognize that analyzing the wealth of data provided by these new sequencing platforms requires careful attention to detail for robust results.  ...  Innovations in sequencing technologies have allowed biologists to make incredible advances in understanding biological systems.  ...  Nancy Lin for feedback during the writing process.  ... 
doi:10.3389/fgene.2015.00235 pmid:26217378 pmcid:PMC4493402 fatcat:fbq2cewm35hqjl24vu6kdrejfy
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