Sewe, Steven, Silva, Goncalo ORCID: https://orcid.org/0000-0001-5544-2947, Sicat, Juan Paolo, Seal, Susan ORCID: https://orcid.org/0000-0002-3952-1562 and Muhindira, Paul Visendi (2022) Trimming and validation of Illumina short reads using Trimmomatic, trinity assembly, and assessment of RNA-Seq Data. In: Edwards, David, (ed.) Plant Bioinformatics. Methods in Molecular Biology. Springer Protocols, 2443 . Humana Press - Springer Nature, New York, United States, pp. 211-232. ISBN 978-1071620663 ; 978-1071620670 (doi:10.1007/978-1-0716-2067-0_11)

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Abstract

Next-generation sequencing (NGS) technologies can generate billions of reads in a single sequencing run. However, with such high-throughput comes quality issues which have to be addressed before undertaking downstream analysis. Quality control on short reads is usually performed at default settings due to a lack of in-depth understanding of a particular software’s parameters and their effect if changed on the output. Here we demonstrate how to optimize read trimming using Trimmomatic. We highlight the benefits of trimming by comparing the quality of transcripts assembled using trimmed and untrimmed reads.

Item Type:	Book Section
Uncontrolled Keywords:	quality control; Illumina adapters; transcriptome assembly; Trimmomatic; trinity; Busco; Fastqc; Quast
Subjects:	Q Science > QH Natural history > QH301 Biology Q Science > QH Natural history > QH426 Genetics S Agriculture > S Agriculture (General)
Faculty / School / Research Centre / Research Group:	Faculty of Engineering & Science Faculty of Engineering & Science > Natural Resources Institute Faculty of Engineering & Science > Natural Resources Institute > Agriculture, Health & Environment Department Faculty of Engineering & Science > Natural Resources Institute > Centre for Sustainable Agriculture 4 One Health Faculty of Engineering & Science > Natural Resources Institute > Centre for Sustainable Agriculture 4 One Health > Molecular Virology & Entomology
Last Modified:	27 Nov 2024 15:18
URI:	http://gala.gre.ac.uk/id/eprint/35572

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