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

2 Citations (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

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

Cite this

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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.",

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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 - https://www.scopus.com/pages/publications/85123364898

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

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M3 - Chapter

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PB - Humana Press Inc.

ER -

Making a Pangenome Using the Iterative Mapping Approach

Abstract

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Plant Bioinformatics: Methods and Protocols

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