Abstract
A high-quality, annotated genome assembly is the foundation for many downstream studies. However, obtaining such an assembly is a complex, reiterative process that requires the assimilation of high-quality data and combines different approaches and data types. While some software packages incorporating multiple steps of genome assembly are commercially available, they may not be flexible enough to be routinely applied to all organisms, particularly to nonmodel species such as pathogenic oomycetes and fungi. If researchers understand and apply the most appropriate, currently available tools for each step, it is possible to customize parameters and optimize results for their organism of study. Based on our experience of de novo assembly and annotation of several oomycete species, this chapter provides a modular workflow from processing of raw reads, to initial assembly generation, through optimization, chromosome-scale scaffolding and annotation, outlining input and output data as well as examples and alternative software used for each step. The accompanying Notes provide background information for each step as well as alternative options. The final result of this workflow could be an annotated, high-quality, validated, chromosome-scale assembly or a draft assembly of sufficient quality to meet specific needs of a project.
| Original language | English (US) |
|---|---|
| Title of host publication | Methods in Molecular Biology |
| Publisher | Humana Press Inc. |
| Pages | 151-197 |
| Number of pages | 47 |
| DOIs | |
| State | Published - Jan 1 2018 |
Publication series
| Name | Methods in Molecular Biology |
|---|---|
| Volume | 1848 |
| ISSN (Print) | 1064-3745 |
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Keywords
- Assembly quality
- Contig scaffolding
- Genome annotation
- Genome assembly
- Hi-C
- Next-generation sequencing
- Optical maps
ASJC Scopus subject areas
- Molecular Biology
- Genetics
Cite this
From short reads to chromosome-scale genome assemblies. / Fletcher, Kyle; Michelmore, Richard W.
Methods in Molecular Biology. Humana Press Inc., 2018. p. 151-197 (Methods in Molecular Biology; Vol. 1848).Research output: Chapter in Book/Report/Conference proceeding › Chapter
}
TY - CHAP
T1 - From short reads to chromosome-scale genome assemblies
AU - Fletcher, Kyle
AU - Michelmore, Richard W
PY - 2018/1/1
Y1 - 2018/1/1
N2 - A high-quality, annotated genome assembly is the foundation for many downstream studies. However, obtaining such an assembly is a complex, reiterative process that requires the assimilation of high-quality data and combines different approaches and data types. While some software packages incorporating multiple steps of genome assembly are commercially available, they may not be flexible enough to be routinely applied to all organisms, particularly to nonmodel species such as pathogenic oomycetes and fungi. If researchers understand and apply the most appropriate, currently available tools for each step, it is possible to customize parameters and optimize results for their organism of study. Based on our experience of de novo assembly and annotation of several oomycete species, this chapter provides a modular workflow from processing of raw reads, to initial assembly generation, through optimization, chromosome-scale scaffolding and annotation, outlining input and output data as well as examples and alternative software used for each step. The accompanying Notes provide background information for each step as well as alternative options. The final result of this workflow could be an annotated, high-quality, validated, chromosome-scale assembly or a draft assembly of sufficient quality to meet specific needs of a project.
AB - A high-quality, annotated genome assembly is the foundation for many downstream studies. However, obtaining such an assembly is a complex, reiterative process that requires the assimilation of high-quality data and combines different approaches and data types. While some software packages incorporating multiple steps of genome assembly are commercially available, they may not be flexible enough to be routinely applied to all organisms, particularly to nonmodel species such as pathogenic oomycetes and fungi. If researchers understand and apply the most appropriate, currently available tools for each step, it is possible to customize parameters and optimize results for their organism of study. Based on our experience of de novo assembly and annotation of several oomycete species, this chapter provides a modular workflow from processing of raw reads, to initial assembly generation, through optimization, chromosome-scale scaffolding and annotation, outlining input and output data as well as examples and alternative software used for each step. The accompanying Notes provide background information for each step as well as alternative options. The final result of this workflow could be an annotated, high-quality, validated, chromosome-scale assembly or a draft assembly of sufficient quality to meet specific needs of a project.
KW - Assembly quality
KW - Contig scaffolding
KW - Genome annotation
KW - Genome assembly
KW - Hi-C
KW - Next-generation sequencing
KW - Optical maps
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U2 - 10.1007/978-1-4939-8724-5_13
DO - 10.1007/978-1-4939-8724-5_13
M3 - Chapter
T3 - Methods in Molecular Biology
SP - 151
EP - 197
BT - Methods in Molecular Biology
PB - Humana Press Inc.
ER -