Plant-Virus Interactions
Springer US
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| Chapter title |
Computational Pipeline for the Detection of Plant RNA Viruses Using High-Throughput Sequencing.
|
|---|---|
| Book title |
Plant-Virus Interactions
|
| Published in |
Methods in molecular biology, January 2024
|
| DOI | 10.1007/978-1-0716-3485-1_1 |
| Pubmed ID | |
| Book ISBNs |
978-1-07-163484-4, 978-1-07-163485-1
|
| Authors |
Donaire, Livia, Aranda, Miguel A, Aranda, Miguel A. |
| Abstract |
In this chapter, we describe a computational pipeline for the in silico detection of plant viruses by high-throughput sequencing (HTS) from total RNA samples. The pipeline is designed for the analysis of short reads generated using an Illumina platform and free-available software tools. First, we provide advice for high-quality total RNA purification, library preparation, and sequencing. The bioinformatics pipeline begins with the raw reads obtained from the sequencing machine and performs some curation steps to obtain long contigs. Contigs are blasted against a local database of reference nucleotide viral sequences to identify the viruses in the samples. Then, the search is refined by applying specific filters. We also provide the code to re-map the short reads against the viruses found to get information on sequencing depth and read coverage for each virus. No previous bioinformatics background is required, but basic knowledge of the Unix command line and R language is recommended. |
X Demographics
The data shown below were collected from the profile of 1 X user who shared this research output. Click here to find out more about how the information was compiled.
Geographical breakdown
| Country | Count | As % |
|---|---|---|
| Unknown | 1 | 100% |
Demographic breakdown
| Type | Count | As % |
|---|---|---|
| Members of the public | 1 | 100% |
Attention Score in Context
This research output has an Altmetric Attention Score of 1. This is our high-level measure of the quality and quantity of online attention that it has received. This Attention Score, as well as the ranking and number of research outputs shown below, was calculated when the research output was last mentioned on 21 November 2023.
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#17,038,804
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#5,919
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Outputs of similar age
#67,003
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Outputs of similar age from Methods in molecular biology
#82
of 197 outputs
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