Pangenome graph construction from genome alignments with Minigraph-Cactus

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

doi:10.1038/s41587-023-01793-w

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Pangenome graph construction from genome alignments with Minigraph-Cactus

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

Publication date (Electronic): May 10 2023

Journal: Nature Biotechnology

Publisher: Springer Science and Business Media LLC

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A global reference for human genetic variation

Lachlan Coin, Robert Garry, Oleksyk Taras (2017)

The 1000 Genomes Project set out to provide a comprehensive description of common human genetic variation by applying whole-genome sequencing to a diverse set of individuals from multiple populations. Here we report completion of the project, having reconstructed the genomes of 2,504 individuals from 26 populations using a combination of low-coverage whole-genome sequencing, deep exome sequencing, and dense microarray genotyping. We characterized a broad spectrum of genetic variation, in total over 88 million variants (84.7 million single nucleotide polymorphisms (SNPs), 3.6 million short insertions/deletions (indels), and 60,000 structural variants), all phased onto high-quality haplotypes. This resource includes >99% of SNP variants with a frequency of >1% for a variety of ancestries. We describe the distribution of genetic variation across the global sample, and discuss the implications for common disease studies.

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Minimap2: pairwise alignment for nucleotide sequences

Heng Li (2018)

Recent advances in sequencing technologies promise ultra-long reads of ∼100 kb in average, full-length mRNA or cDNA reads in high throughput and genomic contigs over 100 Mb in length. Existing alignment programs are unable or inefficient to process such data at scale, which presses for the development of new alignment algorithms.

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Twelve years of SAMtools and BCFtools

Petr Danecek, James Bonfield, Jennifer Liddle … (2021)

Abstract Background SAMtools and BCFtools are widely used programs for processing and analysing high-throughput sequencing data. They include tools for file format conversion and manipulation, sorting, querying, statistics, variant calling, and effect analysis amongst other methods. Findings The first version appeared online 12 years ago and has been maintained and further developed ever since, with many new features and improvements added over the years. The SAMtools and BCFtools packages represent a unique collection of tools that have been used in numerous other software projects and countless genomic pipelines. Conclusion Both SAMtools and BCFtools are freely available on GitHub under the permissive MIT licence, free for both non-commercial and commercial use. Both packages have been installed >1 million times via Bioconda. The source code and documentation are available from https://www.htslib.org.