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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)
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Wagner, Justin (author)
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McDaniel, Jennifer (author)
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show more...
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Stephens, Sarah H. (author)
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Westreich, Samuel T. (author)
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Prasanna, Anish G. (author)
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Johanson, Elaine (author)
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Maier, Ezekiel J. (author)
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Boja, Emily (author)
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Serang, Omar (author)
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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,Transl onkogenomik,Sektion I,Institutionen för kliniska vetenskaper, Lund,Medicinska fakulteten,Lund University Research Groups,LUCC: Lund University Cancer Centre,Other Strong Research Environments,Transl oncogenomics,Section I,Department of Clinical Sciences, Lund,Faculty of Medicine
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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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(creator_code:org_t)
- Cold Spring Harbor Laboratory, 2020
- English.
- Related links:
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http://dx.doi.org/10... (free)
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https://www.biorxiv....
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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
Close
- The precisionFDA Truth Challenge V2 aimed to assess the state-of-the-art of variant calling in difficult-to-map regions and the Major Histocompatibility Complex (MHC). Starting with FASTQ files, 20 challenge participants applied their variant calling pipelines and submitted 64 variant callsets for one or more sequencing technologies (~35X Illumina, ~35X PacBio HiFi, and ~50X Oxford Nanopore Technologies). Submissions were evaluated following best practices for benchmarking small variants with the new GIAB benchmark sets and genome stratifications. Challenge submissions included a number of innovative methods for all three technologies, with graph-based and machine-learning methods scoring best for short-read and long-read datasets, respectively. New methods out-performed the 2016 Truth Challenge winners, and new 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
- short-read sequencing
- long-read sequencing
- benchmark
Publication and Content Type
- ovr (subject category)
- vet (subject category)
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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Maier, Ezekiel J ...
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Boja, Emily
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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
- By the university
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Lund University