Local read haplotagging enables accurate long-read small variant calling

Autor: Alexey Kolesnikov, Daniel Cook, Maria Nattestad, Lucas Brambrink, Brandy McNulty, John Gorzynski, Sneha Goenka, Euan A. Ashley, Miten Jain, Karen H. Miga, Benedict Paten, Pi-Chuan Chang, Andrew Carroll, Kishwar Shafin

Publikováno v: Nature Communications, Vol 15, Iss 1, Pp 1-12 (2024)

Abstract Long-read sequencing technology has enabled variant detection in difficult-to-map regions of the genome and enabled rapid genetic diagnosis in clinical settings. Rapidly evolving third-generation sequencing platforms like Pacific Biosciences

Externí odkaz: https://doaj.org/article/9736ff93823742a28239875aa6195f95

A draft human pangenome reference

Autor: Wen-Wei Liao, Mobin Asri, Jana Ebler, Daniel Doerr, Marina Haukness, Glenn Hickey, Shuangjia Lu, Julian K. Lucas, Jean Monlong, Haley J. Abel, Silvia Buonaiuto, Xian H. Chang, Haoyu Cheng, Justin Chu, Vincenza Colonna, Jordan M. Eizenga, Xiaowen Feng, Christian Fischer, Robert S. Fulton, Shilpa Garg, Cristian Groza, Andrea Guarracino, William T. Harvey, Simon Heumos, Kerstin Howe, Miten Jain, Tsung-Yu Lu, Charles Markello, Fergal J. Martin, Matthew W. Mitchell, Katherine M. Munson, Moses Njagi Mwaniki, Adam M. Novak, Hugh E. Olsen, Trevor Pesout, David Porubsky, Pjotr Prins, Jonas A. Sibbesen, Jouni Sirén, Chad Tomlinson, Flavia Villani, Mitchell R. Vollger, Lucinda L. Antonacci-Fulton, Gunjan Baid, Carl A. Baker, Anastasiya Belyaeva, Konstantinos Billis, Andrew Carroll, Pi-Chuan Chang, Sarah Cody, Daniel E. Cook, Robert M. Cook-Deegan, Omar E. Cornejo, Mark Diekhans, Peter Ebert, Susan Fairley, Olivier Fedrigo, Adam L. Felsenfeld, Giulio Formenti, Adam Frankish, Yan Gao, Nanibaa’ A. Garrison, Carlos Garcia Giron, Richard E. Green, Leanne Haggerty, Kendra Hoekzema, Thibaut Hourlier, Hanlee P. Ji, Eimear E. Kenny, Barbara A. Koenig, Alexey Kolesnikov, Jan O. Korbel, Jennifer Kordosky, Sergey Koren, HoJoon Lee, Alexandra P. Lewis, Hugo Magalhães, Santiago Marco-Sola, Pierre Marijon, Ann McCartney, Jennifer McDaniel, Jacquelyn Mountcastle, Maria Nattestad, Sergey Nurk, Nathan D. Olson, Alice B. Popejoy, Daniela Puiu, Mikko Rautiainen, Allison A. Regier, Arang Rhie, Samuel Sacco, Ashley D. Sanders, Valerie A. Schneider, Baergen I. Schultz, Kishwar Shafin, Michael W. Smith, Heidi J. Sofia, Ahmad N. Abou Tayoun, Françoise Thibaud-Nissen, Francesca Floriana Tricomi, Justin Wagner, Brian Walenz, Jonathan M. D. Wood, Aleksey V. Zimin, Guillaume Bourque, Mark J. P. Chaisson, Paul Flicek, Adam M. Phillippy, Justin M. Zook, Evan E. Eichler, David Haussler, Ting Wang, Erich D. Jarvis, Karen H. Miga, Erik Garrison, Tobias Marschall, Ira M. Hall, Heng Li, Benedict Paten

Publikováno v: Nature. 617:312-324

Here the Human Pangenome Reference Consortium presents a first draft of the human pangenome reference. The pangenome contains 47 phased, diploid assemblies from a cohort of genetically diverse individuals1. These assemblies cover more than 99% of the

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::ce56c54eebc15371aabecb5595f996d0
https://doi.org/10.1038/s41586-023-05896-x

DeepConsensus improves the accuracy of sequences with a gap-aware sequence transformer

Autor: Gunjan Baid, Daniel E. Cook, Kishwar Shafin, Taedong Yun, Felipe Llinares-López, Quentin Berthet, Anastasiya Belyaeva, Armin Töpfer, Aaron M. Wenger, William J. Rowell, Howard Yang, Alexey Kolesnikov, Waleed Ammar, Jean-Philippe Vert, Ashish Vaswani, Cory Y. McLean, Maria Nattestad, Pi-Chuan Chang, Andrew Carroll

Publikováno v: Nature Biotechnology.

Circular consensus sequencing with Pacific Biosciences (PacBio) technology generates long (10-25 kilobases), accurate 'HiFi' reads by combining serial observations of a DNA molecule into a consensus sequence. The standard approach to consensus genera

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::25477d49598b3d1ad79103576e4cdcc8
https://doi.org/10.1038/s41587-022-01435-7

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

Autor: Nathan D. Olson, Justin Wagner, Jennifer McDaniel, Sarah H. Stephens, Samuel T. Westreich, Anish G. Prasanna, Elaine Johanson, Emily Boja, Ezekiel J. Maier, Omar Serang, David Jáspez, José M. Lorenzo-Salazar, Adrián Muñoz-Barrera, Luis A. Rubio-Rodríguez, Carlos Flores, Konstantinos Kyriakidis, Andigoni Malousi, Kishwar Shafin, Trevor Pesout, Miten Jain, Benedict Paten, Pi-Chuan Chang, Alexey Kolesnikov, Maria Nattestad, Gunjan Baid, Sidharth Goel, Howard Yang, Andrew Carroll, Robert Eveleigh, Mathieu Bourgey, Guillaume Bourque, Gen Li, ChouXian Ma, LinQi Tang, YuanPing Du, ShaoWei Zhang, Jordi Morata, Raúl Tonda, Genís Parra, Jean-Rémi Trotta, Christian Brueffer, Sinem Demirkaya-Budak, Duygu Kabakci-Zorlu, Deniz Turgut, Özem Kalay, Gungor Budak, Kübra Narcı, Elif Arslan, Richard Brown, Ivan J. Johnson, Alexey Dolgoborodov, Vladimir Semenyuk, Amit Jain, H. Serhat Tetikol, Varun Jain, Mike Ruehle, Bryan Lajoie, Cooper Roddey, Severine Catreux, Rami Mehio, Mian Umair Ahsan, Qian Liu, Kai Wang, Sayed Mohammad Ebrahim Sahraeian, Li Tai Fang, Marghoob Mohiyuddin, Calvin Hung, Chirag Jain, Hanying Feng, Zhipan Li, Luoqi Chen, Fritz J. Sedlazeck, Justin M. Zook

Publikováno v: Cell genomics. 2(5)

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

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::5a3e674f44cc6612dde91b563790f800
https://pubmed.ncbi.nlm.nih.gov/35720974

DeepTrio: Variant Calling in Families Using Deep Learning

Autor: Andrew Carroll, Pi-Chuan Chang, Sidharth Goel, Howard Yang, Taedong Yun, Alexey Kolesnikov, Gunjan Baid, Maria Nattestad, Cory Y. McLean

Every human inherits one copy of the genome from their mother and another from their father. Parental inheritance helps us understand the transmission of traits and genetic diseases, which often involve de novo variants and rare recessive alleles. He

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_________::0f2bf16c653dfd975a3fe1a8686554e4
https://doi.org/10.1101/2021.04.05.438434