PrecisionFDA Truth Challenge V2: Calling variants from short and long reads in difficult-to-map regions

↓ Direkt till sidans innehåll
↓ Direkt till sidans sekundära innehåll (sidomenyn)

Search: WFRF:(Ma Shaowei) > PrecisionFDA Truth ...

Details
MARC

Olson, Nathan D.National Institute of Standards and Technology (NIST) (author)

PrecisionFDA Truth Challenge V2: Calling variants from short and long reads in difficult-to-map regions

Article/chapterEnglish2022

Publisher, publication year, extent ...

Elsevier BV,2022

Numbers

LIBRIS-ID:oai:lup.lub.lu.se:321a29e2-0c7d-4659-90cc-e5a073131432
https://lup.lub.lu.se/record/321a29e2-0c7d-4659-90cc-e5a073131432URI
https://doi.org/10.1016/j.xgen.2022.100129DOI

Supplementary language notes

Language:English
Summary in:English

Part of subdatabase

SwePubSwePub

Classification

Subject category:art swepub-publicationtype
Subject category:ref swepub-contenttype

Notes

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 and genre

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
DNA
variant
shot-read sequencing
long-read sequencing
benchmark

Added entries (persons, corporate bodies, meetings, titles ...)

Wagner, JustinNational Institute of Standards and Technology (NIST) (author)
McDaniel, JenniferNational Institute of Standards and Technology (NIST) (author)
Stephens, Sarah H.Booz Allen Hamilton, Inc. (author)
Westreich, Samuel T.DNAnexus (author)
Prasanna, Anish G.Booz Allen Hamilton, Inc. (author)
Johanson, ElaineUnited States Food and Drug Administration (author)
Boja, EmilyUnited States Food and Drug Administration (author)
Maier, Ezekiel J.Booz Allen Hamilton, Inc. (author)
Serang, OmarDNAnexus (author)
Jáspez, David (author)
Lorenzo-Salazar, José M. (author)
Muñoz-Barrera, Adrián (author)
Rubio-Rodríguez, Luis A. (author)
Flores, Carlos (author)
Kyriakidis, Konstantinos (author)
Malousi, Andigoni (author)
Shafin, Kishwar (author)
Pesout, Trevor (author)
Jain, Miten (author)
Paten, Benedict (author)
Chang, Pi-Chuan (author)
Kolesnikov, Alexey (author)
Nattestad, Maria (author)
Baid, Gunjan (author)
Goel, Sidharth (author)
Yang, Howard (author)
Carroll, Andrew (author)
Eveleigh, Robert (author)
Bourgey, Mathieu (author)
Bourque, Guillaume (author)
Li, Gen (author)
MA, ChouXian (author)
Tang, LinQi (author)
DU, YuanPing (author)
Zhang, ShaoWei (author)
Morata, Jordi (author)
Tonda, Raúl (author)
Parra, Genís (author)
Trotta, Jean-Rémi (author)
Brueffer, ChristianLund 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(Swepub:lu)med-csb (author)
Demirkaya-Budak, Sinem (author)
Kabakci-Zorlu, Duygu (author)
Turgut, Deniz (author)
Kalay, Özem (author)
Budak, Gungor (author)
Narcı, Kübra (author)
Arslan, Elif (author)
Brown, Richard (author)
Johnson, Ivan J. (author)
Dolgoborodov, Alexey (author)
Semenyuk, Vladimir (author)
Jain, Amit (author)
Tetikol, H. Serhat (author)
Jain, Varun (author)
Ruehle, Mike (author)
Lajoie, Bryan (author)
Roddey, Cooper (author)
Catreux, Severine (author)
Mehio, Rami (author)
Ahsan, Mian Umair (author)
Liu, Qian (author)
Wang, Kai (author)
Sahraeian, Sayed Mohammad Ebrahim (author)
Fang, Li Tai (author)
Mohiyuddin, Marghoob (author)
Hung, Calvin (author)
Jain, Chirag (author)
Feng, Hanying (author)
Li, Zhipan (author)
Chen, Luoqi (author)
Sedlazeck, Fritz J. (author)
Zook, Justin M (author)
National Institute of Standards and Technology (NIST)Booz Allen Hamilton, Inc. (creator_code:org_t)

Related titles

In:Cell Genomics: Elsevier BV2:5, s. 1-122666-979X

Internet link

Find in a library

Cell Genomics (Search for host publication in LIBRIS)

To the university's database

Find more in SwePub

By the author/editor: Olson, Nathan D.; Wagner, Justin; McDaniel, Jennif ...; Stephens, Sarah ...; Westreich, Samue ...; Prasanna, Anish ...; show more...; Johanson, Elaine; Boja, Emily; Maier, Ezekiel J ...; Serang, Omar; Jáspez, David; Lorenzo-Salazar, ...; Muñoz-Barrera, A ...; Rubio-Rodríguez, ...; Flores, Carlos; Kyriakidis, Kons ...; Malousi, Andigon ...; Shafin, Kishwar; Pesout, Trevor; Jain, Miten; Paten, Benedict; Chang, Pi-Chuan; Kolesnikov, Alex ...; Nattestad, Maria; Baid, Gunjan; Goel, Sidharth; Yang, Howard; Carroll, Andrew; Eveleigh, Robert; Bourgey, Mathieu; Bourque, Guillau ...; Li, Gen; MA, ChouXian; Tang, LinQi; DU, YuanPing; Zhang, ShaoWei; Morata, Jordi; Tonda, Raúl; Parra, Genís; Trotta, Jean-Rém ...; Brueffer, Christ ...; Demirkaya-Budak, ...; Kabakci-Zorlu, D ...; Turgut, Deniz; Kalay, Özem; Budak, Gungor; Narcı, Kübra; Arslan, Elif; Brown, Richard; Johnson, Ivan J.; Dolgoborodov, Al ...; Semenyuk, Vladim ...; Jain, Amit; Tetikol, H. Serh ...; Jain, Varun; Ruehle, Mike; Lajoie, Bryan; Roddey, Cooper; Catreux, Severin ...; Mehio, Rami; Ahsan, Mian Umai ...; Liu, Qian; Wang, Kai; Sahraeian, Sayed ...; Fang, Li Tai; Mohiyuddin, Marg ...; Hung, Calvin; Jain, Chirag; Feng, Hanying; Li, Zhipan; Chen, Luoqi; Sedlazeck, Fritz ...; Zook, Justin M; show less...

About the subject

NATURAL SCIENCES: NATURAL SCIENCES; and Biological Scien ...; and Bioinformatics a ...

NATURAL SCIENCES: NATURAL SCIENCES; and Computer and Inf ...; and Bioinformatics

MEDICAL AND HEALTH SCIENCES: MEDICAL AND HEAL ...; and Basic Medicine; and Medical Genetics

Articles in the publication: Cell Genomics

By the university: Lund University

Search outside SwePub

Extend your search to:: Google; Google Book Search; Google Scholar

Kungliga biblioteket hanterar dina personuppgifter i enlighet med EU:s dataskyddsförordning (2018), GDPR. Läs mer om hur det funkar här.
Så här hanterar KB dina uppgifter vid användning av denna tjänst.

LIBRIS.kb.se