Making a Pangenome Using the Iterative Mapping Approach

Cassandria Tay Fernandez

doi:10.1007/978-1-0716-2067-0_14

Making a Pangenome Using the Iterative Mapping Approach

Cassandria Tay Fernandez

School of Biological Sciences

Research output: Chapter in Book/Conference paper › Chapter › peer-review

1 Citation (Scopus)

Abstract

Pangenomes have replaced single reference genomes as genetic references, as they contain a better scope of the diversity found in a single species. This protocol outlines the iterative mapping approach in constructing a pangenome, including how to check the raw data, align the data to a reference, how to assemble the data, and how to remove potential contaminants from the final assembly.

Original language	English
Title of host publication	Plant Bioinformatics
Subtitle of host publication	Methods and Protocols
Editors	David Edwards
Publisher	Humana Press Inc.
Chapter	14
Pages	259-271
Number of pages	13
Volume	2443
Edition	3rd
ISBN (Electronic)	978-1-0716-2067-0
ISBN (Print)	978-1-0716-2066-3
DOIs	https://doi.org/10.1007/978-1-0716-2067-0_14
Publication status	Published - 2022

Publication series

Name	Methods in Molecular Biology
Volume	2443
ISSN (Print)	1064-3745
ISSN (Electronic)	1940-6029

Access to Document

10.1007/978-1-0716-2067-0_14

Cite this

@inbook{8db0e23336074511848e77638153505a,

title = "Making a Pangenome Using the Iterative Mapping Approach",

abstract = "Pangenomes have replaced single reference genomes as genetic references, as they contain a better scope of the diversity found in a single species. This protocol outlines the iterative mapping approach in constructing a pangenome, including how to check the raw data, align the data to a reference, how to assemble the data, and how to remove potential contaminants from the final assembly.",

keywords = "Bioinformatics, Iterative mapping, Pangenome, Pangenomics, Plant genome",

author = "{Tay Fernandez}, Cassandria",

note = "Publisher Copyright: {\textcopyright} 2022, The Author(s), under exclusive license to Springer Science+Business Media, LLC, part of Springer Nature.",

year = "2022",

doi = "10.1007/978-1-0716-2067-0_14",

language = "English",

isbn = "978-1-0716-2066-3",

volume = "2443",

series = "Methods in Molecular Biology",

publisher = "Humana Press Inc.",

pages = "259--271",

editor = "David Edwards",

booktitle = "Plant Bioinformatics",

address = "United States",

edition = "3rd",

}

TY - CHAP

T1 - Making a Pangenome Using the Iterative Mapping Approach

AU - Tay Fernandez, Cassandria

PY - 2022

Y1 - 2022

N2 - Pangenomes have replaced single reference genomes as genetic references, as they contain a better scope of the diversity found in a single species. This protocol outlines the iterative mapping approach in constructing a pangenome, including how to check the raw data, align the data to a reference, how to assemble the data, and how to remove potential contaminants from the final assembly.

AB - Pangenomes have replaced single reference genomes as genetic references, as they contain a better scope of the diversity found in a single species. This protocol outlines the iterative mapping approach in constructing a pangenome, including how to check the raw data, align the data to a reference, how to assemble the data, and how to remove potential contaminants from the final assembly.

KW - Bioinformatics

KW - Iterative mapping

KW - Pangenome

KW - Pangenomics

KW - Plant genome

UR - http://www.scopus.com/inward/record.url?scp=85123364898&partnerID=8YFLogxK

UR - https://link.springer.com/book/10.1007/978-1-4939-3167-5#toc

U2 - 10.1007/978-1-0716-2067-0_14

DO - 10.1007/978-1-0716-2067-0_14

M3 - Chapter

C2 - 35037211

AN - SCOPUS:85123364898

SN - 978-1-0716-2066-3

VL - 2443

T3 - Methods in Molecular Biology

SP - 259

EP - 271

BT - Plant Bioinformatics

A2 - Edwards, David

PB - Humana Press Inc.

ER -

Making a Pangenome Using the Iterative Mapping Approach

Abstract

Publication series

Access to Document

Other files and links

Fingerprint

Plant Bioinformatics: Methods and Protocols

Cite this