Trimming and Validation of Illumina Short Reads Using Trimmomatic, Trinity Assembly, and Assessment of RNA-Seq Data

Steven O Sewe; Gonçalo Silva; Paulo Sicat; Susan E Seal; Paul Visendi

doi:10.1007/978-1-0716-2067-0_11

Trimming and Validation of Illumina Short Reads Using Trimmomatic, Trinity Assembly, and Assessment of RNA-Seq Data

Methods Mol Biol. 2022:2443:211-232. doi: 10.1007/978-1-0716-2067-0_11.

Authors

Steven O Sewe¹, Gonçalo Silva¹, Paulo Sicat¹, Susan E Seal¹, Paul Visendi²

Affiliations

¹ Natural Resources Institute, University of Greenwich, Kent, UK.
² Centre for Agriculture and the Bioeconomy, Queensland University of Technology, Brisbane, QLD, Australia. paul.muhindira@qut.edu.au.

PMID: 35037208
DOI: 10.1007/978-1-0716-2067-0_11

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.

Keywords: Busco; Fastqc; Illumina adapters; Quality control; Quast; Transcriptome assembly; Trimmomatic; Trinity.

MeSH terms

Computational Biology*
Exome Sequencing
High-Throughput Nucleotide Sequencing*
Quality Control
RNA-Seq