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PrecisionFDA Truth ...
PrecisionFDA Truth Challenge V2: Calling variants from short and long reads in difficult-to-map regions
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- Olson, Nathan D. (author)
- National Institute of Standards and Technology (NIST)
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- Wagner, Justin (author)
- National Institute of Standards and Technology (NIST)
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- McDaniel, Jennifer (author)
- National Institute of Standards and Technology (NIST)
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show more...
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- Stephens, Sarah H. (author)
- Booz Allen Hamilton, Inc.
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- Westreich, Samuel T. (author)
- DNAnexus
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- Prasanna, Anish G. (author)
- Booz Allen Hamilton, Inc.
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- Johanson, Elaine (author)
- United States Food and Drug Administration
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- Boja, Emily (author)
- United States Food and Drug Administration
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- Maier, Ezekiel J. (author)
- Booz Allen Hamilton, Inc.
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- Serang, Omar (author)
- DNAnexus
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Jáspez, David (author)
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Lorenzo-Salazar, José M. (author)
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Muñoz-Barrera, Adrián (author)
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Rubio-Rodríguez, Luis A. (author)
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Flores, Carlos (author)
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Kyriakidis, Konstantinos (author)
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Malousi, Andigoni (author)
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Shafin, Kishwar (author)
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Pesout, Trevor (author)
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Jain, Miten (author)
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Paten, Benedict (author)
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Chang, Pi-Chuan (author)
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Kolesnikov, Alexey (author)
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Nattestad, Maria (author)
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Baid, Gunjan (author)
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Goel, Sidharth (author)
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Yang, Howard (author)
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Carroll, Andrew (author)
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Eveleigh, Robert (author)
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Bourgey, Mathieu (author)
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Bourque, Guillaume (author)
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Li, Gen (author)
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MA, ChouXian (author)
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Tang, LinQi (author)
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DU, YuanPing (author)
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Zhang, ShaoWei (author)
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Morata, Jordi (author)
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Tonda, Raúl (author)
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Parra, Genís (author)
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Trotta, Jean-Rémi (author)
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- Brueffer, Christian (author)
- Lund University,Lunds universitet,Translational Oncogenomics,Forskargrupper vid Lunds universitet,LUCC: Lunds universitets cancercentrum,Övriga starka forskningsmiljöer,Lund University Research Groups,LUCC: Lund University Cancer Centre,Other Strong Research Environments
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Demirkaya-Budak, Sinem (author)
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Kabakci-Zorlu, Duygu (author)
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Turgut, Deniz (author)
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Kalay, Özem (author)
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Budak, Gungor (author)
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Narcı, Kübra (author)
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Arslan, Elif (author)
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Brown, Richard (author)
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Johnson, Ivan J. (author)
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Dolgoborodov, Alexey (author)
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Semenyuk, Vladimir (author)
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Jain, Amit (author)
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Tetikol, H. Serhat (author)
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Jain, Varun (author)
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Ruehle, Mike (author)
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Lajoie, Bryan (author)
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Roddey, Cooper (author)
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Catreux, Severine (author)
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Mehio, Rami (author)
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Ahsan, Mian Umair (author)
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Liu, Qian (author)
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Wang, Kai (author)
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Sahraeian, Sayed Mohammad Ebrahim (author)
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Fang, Li Tai (author)
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Mohiyuddin, Marghoob (author)
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Hung, Calvin (author)
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Jain, Chirag (author)
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Feng, Hanying (author)
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Li, Zhipan (author)
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Chen, Luoqi (author)
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Sedlazeck, Fritz J. (author)
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Zook, Justin M (author)
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National Institute of Standards and Technology (NIST) Booz Allen Hamilton, Inc (creator_code:org_t)
- Elsevier BV, 2022
- 2022
- English.
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In: Cell Genomics. - : Elsevier BV. - 2666-979X. ; 2:5, s. 1-12
- Related links:
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http://dx.doi.org/10... (free)
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https://lup.lub.lu.s...
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https://doi.org/10.1...
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Abstract
Subject headings
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- The precisionFDA Truth Challenge V2 aimed to assess the state of the art of variant calling in challenging genomic regions. Starting with FASTQs, 20 challenge participants applied their variant-calling pipelines and submitted 64 variant call sets for one or more sequencing technologies (Illumina, PacBio HiFi, and Oxford Nanopore Technologies). Submissions were evaluated following best practices for benchmarking small variants with updated Genome in a Bottle benchmark sets and genome stratifications. Challenge submissions included numerous innovative methods, with graph-based and machine learning methods scoring best for short-read and long-read datasets, respectively. With machine learning approaches, combining multiple sequencing technologies performed particularly well. Recent developments in sequencing and variant calling have enabled benchmarking variants in challenging genomic regions, paving the way for the identification of previously unknown clinically relevant variants.
Subject headings
- NATURVETENSKAP -- Biologi -- Bioinformatik och systembiologi (hsv//swe)
- NATURAL SCIENCES -- Biological Sciences -- Bioinformatics and Systems Biology (hsv//eng)
- NATURVETENSKAP -- Data- och informationsvetenskap -- Bioinformatik (hsv//swe)
- NATURAL SCIENCES -- Computer and Information Sciences -- Bioinformatics (hsv//eng)
- MEDICIN OCH HÄLSOVETENSKAP -- Medicinska och farmaceutiska grundvetenskaper -- Medicinsk genetik (hsv//swe)
- MEDICAL AND HEALTH SCIENCES -- Basic Medicine -- Medical Genetics (hsv//eng)
Keyword
- DNA
- variant
- shot-read sequencing
- long-read sequencing
- benchmark
Publication and Content Type
- art (subject category)
- ref (subject category)
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To the university's database
- By the author/editor
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Olson, Nathan D.
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Wagner, Justin
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McDaniel, Jennif ...
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Stephens, Sarah ...
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Westreich, Samue ...
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Prasanna, Anish ...
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show more...
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Johanson, Elaine
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Boja, Emily
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Maier, Ezekiel J ...
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Serang, Omar
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Jáspez, David
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Lorenzo-Salazar, ...
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Muñoz-Barrera, A ...
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Rubio-Rodríguez, ...
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Flores, Carlos
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Kyriakidis, Kons ...
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Malousi, Andigon ...
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Shafin, Kishwar
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Pesout, Trevor
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Jain, Miten
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Paten, Benedict
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Chang, Pi-Chuan
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Kolesnikov, Alex ...
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Nattestad, Maria
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Baid, Gunjan
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Goel, Sidharth
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Yang, Howard
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Carroll, Andrew
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Eveleigh, Robert
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Bourgey, Mathieu
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Bourque, Guillau ...
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Li, Gen
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MA, ChouXian
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Tang, LinQi
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DU, YuanPing
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Zhang, ShaoWei
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Morata, Jordi
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Tonda, Raúl
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Parra, Genís
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Trotta, Jean-Rém ...
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Brueffer, Christ ...
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Demirkaya-Budak, ...
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Kabakci-Zorlu, D ...
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Turgut, Deniz
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Kalay, Özem
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Budak, Gungor
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Narcı, Kübra
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Arslan, Elif
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Brown, Richard
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Johnson, Ivan J.
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Dolgoborodov, Al ...
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Semenyuk, Vladim ...
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Jain, Amit
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Tetikol, H. Serh ...
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Jain, Varun
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Ruehle, Mike
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Lajoie, Bryan
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Roddey, Cooper
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Catreux, Severin ...
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Mehio, Rami
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Ahsan, Mian Umai ...
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Liu, Qian
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Wang, Kai
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Sahraeian, Sayed ...
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Fang, Li Tai
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Mohiyuddin, Marg ...
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Hung, Calvin
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Jain, Chirag
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Feng, Hanying
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Li, Zhipan
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Chen, Luoqi
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Sedlazeck, Fritz ...
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Zook, Justin M
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- About the subject
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- NATURAL SCIENCES
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NATURAL SCIENCES
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and Biological Scien ...
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and Bioinformatics a ...
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- NATURAL SCIENCES
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NATURAL SCIENCES
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and Computer and Inf ...
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and Bioinformatics
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- MEDICAL AND HEALTH SCIENCES
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MEDICAL AND HEAL ...
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and Basic Medicine
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and Medical Genetics
- Articles in the publication
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Cell Genomics
- By the university
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Lund University