Literature DB >> 35496797

Detecting archaic introgression and modeling multiple-wave admixture with ArchaicSeeker 2.0.

Rui Zhang1, Kai Yuan1, Shuhua Xu2,3,4.   

Abstract

ArchaicSeeker 2.0 is designed to identify the sequences derived from known or unknown archaic hominins and to further model the multiple-wave gene flows. The main functional modules involve seeking introgressed sequences, determining corresponding ancestries, and reconstructing the admixture history. The protocol below describes the analytic steps for the application of ArchaicSeeker 2.0 into analysis of example data of the Han Chinese population. For complete details on the use and execution of this protocol, please refer to Yuan et al. (2021).
© 2022 The Author(s).

Entities:  

Keywords:  Bioinformatics; Genetics; Sequence analysis

Mesh：

Year:  2022        PMID： 35496797      PMCID： PMC9038769          DOI： 10.1016/j.xpro.2022.101314

Source DB:  PubMed          Journal:  STAR Protoc        ISSN： 2666-1667


  13 in total

1.  A One-Penny Imputed Genome from Next-Generation Reference Panels.

Authors:  Brian L Browning; Ying Zhou; Sharon R Browning
Journal:  Am J Hum Genet       Date:  2018-08-09       Impact factor: 11.025

2.  MultiWaver 2.0: modeling discrete and continuous gene flow to reconstruct complex population admixtures.

Authors:  Xumin Ni; Kai Yuan; Chang Liu; Qidi Feng; Lei Tian; Zhiming Ma; Shuhua Xu
Journal:  Eur J Hum Genet       Date:  2018-09-11       Impact factor: 4.246

3.  A high-coverage genome sequence from an archaic Denisovan individual.

Authors:  Matthias Meyer; Martin Kircher; Marie-Theres Gansauge; Heng Li; Fernando Racimo; Swapan Mallick; Joshua G Schraiber; Flora Jay; Kay Prüfer; Cesare de Filippo; Peter H Sudmant; Can Alkan; Qiaomei Fu; Ron Do; Nadin Rohland; Arti Tandon; Michael Siebauer; Richard E Green; Katarzyna Bryc; Adrian W Briggs; Udo Stenzel; Jesse Dabney; Jay Shendure; Jacob Kitzman; Michael F Hammer; Michael V Shunkov; Anatoli P Derevianko; Nick Patterson; Aida M Andrés; Evan E Eichler; Montgomery Slatkin; David Reich; Janet Kelso; Svante Pääbo
Journal:  Science       Date:  2012-08-30       Impact factor: 47.728

4.  Identifying and Interpreting Apparent Neanderthal Ancestry in African Individuals.

Authors:  Lu Chen; Aaron B Wolf; Wenqing Fu; Liming Li; Joshua M Akey
Journal:  Cell       Date:  2020-01-30       Impact factor: 41.582

5.  Initial sequence of the chimpanzee genome and comparison with the human genome.

Authors: 
Journal:  Nature       Date:  2005-09-01       Impact factor: 49.962

6.  The complete genome sequence of a Neanderthal from the Altai Mountains.

Authors:  Kay Prüfer; Fernando Racimo; Nick Patterson; Flora Jay; Sriram Sankararaman; Susanna Sawyer; Anja Heinze; Gabriel Renaud; Peter H Sudmant; Cesare de Filippo; Heng Li; Swapan Mallick; Michael Dannemann; Qiaomei Fu; Martin Kircher; Martin Kuhlwilm; Michael Lachmann; Matthias Meyer; Matthias Ongyerth; Michael Siebauer; Christoph Theunert; Arti Tandon; Priya Moorjani; Joseph Pickrell; James C Mullikin; Samuel H Vohr; Richard E Green; Ines Hellmann; Philip L F Johnson; Hélène Blanche; Howard Cann; Jacob O Kitzman; Jay Shendure; Evan E Eichler; Ed S Lein; Trygve E Bakken; Liubov V Golovanova; Vladimir B Doronichev; Michael V Shunkov; Anatoli P Derevianko; Bence Viola; Montgomery Slatkin; David Reich; Janet Kelso; Svante Pääbo
Journal:  Nature       Date:  2013-12-18       Impact factor: 49.962

7.  GenomeWarp: an alignment-based variant coordinate transformation.

Authors:  Cory Y McLean; Yeongwoo Hwang; Ryan Poplin; Mark A DePristo
Journal:  Bioinformatics       Date:  2019-11-01       Impact factor: 6.937

8.  The UCSC genome browser and associated tools.

Authors:  Robert M Kuhn; David Haussler; W James Kent
Journal:  Brief Bioinform       Date:  2012-08-20       Impact factor: 11.622

9.  A general approach for haplotype phasing across the full spectrum of relatedness.

Authors:  Jared O'Connell; Deepti Gurdasani; Olivier Delaneau; Nicola Pirastu; Sheila Ulivi; Massimiliano Cocca; Michela Traglia; Jie Huang; Jennifer E Huffman; Igor Rudan; Ruth McQuillan; Ross M Fraser; Harry Campbell; Ozren Polasek; Gershim Asiki; Kenneth Ekoru; Caroline Hayward; Alan F Wright; Veronique Vitart; Pau Navarro; Jean-Francois Zagury; James F Wilson; Daniela Toniolo; Paolo Gasparini; Nicole Soranzo; Manjinder S Sandhu; Jonathan Marchini
Journal:  PLoS Genet       Date:  2014-04-17       Impact factor: 5.917

10.  The Simons Genome Diversity Project: 300 genomes from 142 diverse populations.

Authors:  Swapan Mallick; Heng Li; Mark Lipson; Iain Mathieson; Melissa Gymrek; Fernando Racimo; Mengyao Zhao; Niru Chennagiri; Susanne Nordenfelt; Arti Tandon; Pontus Skoglund; Iosif Lazaridis; Sriram Sankararaman; Qiaomei Fu; Nadin Rohland; Gabriel Renaud; Yaniv Erlich; Thomas Willems; Carla Gallo; Jeffrey P Spence; Yun S Song; Giovanni Poletti; Francois Balloux; George van Driem; Peter de Knijff; Irene Gallego Romero; Aashish R Jha; Doron M Behar; Claudio M Bravi; Cristian Capelli; Tor Hervig; Andres Moreno-Estrada; Olga L Posukh; Elena Balanovska; Oleg Balanovsky; Sena Karachanak-Yankova; Hovhannes Sahakyan; Draga Toncheva; Levon Yepiskoposyan; Chris Tyler-Smith; Yali Xue; M Syafiq Abdullah; Andres Ruiz-Linares; Cynthia M Beall; Anna Di Rienzo; Choongwon Jeong; Elena B Starikovskaya; Ene Metspalu; Jüri Parik; Richard Villems; Brenna M Henn; Ugur Hodoglugil; Robert Mahley; Antti Sajantila; George Stamatoyannopoulos; Joseph T S Wee; Rita Khusainova; Elza Khusnutdinova; Sergey Litvinov; George Ayodo; David Comas; Michael F Hammer; Toomas Kivisild; William Klitz; Cheryl A Winkler; Damian Labuda; Michael Bamshad; Lynn B Jorde; Sarah A Tishkoff; W Scott Watkins; Mait Metspalu; Stanislav Dryomov; Rem Sukernik; Lalji Singh; Kumarasamy Thangaraj; Svante Pääbo; Janet Kelso; Nick Patterson; David Reich
Journal:  Nature       Date:  2016-09-21       Impact factor: 49.962
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