Table 2.

Most commonly used programs/algorithms for QC protocol.

Software	Reference	Available at
FastQC	[230]	https://www.bioinformatics.babraham.ac.uk/projects/fastqc/ (accessed on 28 June 2022)
Trimmomatic	[231]
Trim Galore	[232]	https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/ (accessed on 28 June 2022)
Cutadapt	[233]	https://journal.embnet.org/index.php/embnetjournal/article/view/200/479 (accessed on 28 June 2022)
CLC Genomics Workbench (Qiagen)	[234]	https://digitalinsights.qiagen.com/products-overview/discovery-insights-portfolio/qiagen-clc-genomics/ (accessed on 28 June 2022)
BBDuk (part of BBTools/BBMap package)	[235]	https://jgi.doe.gov/data-and-tools/software-tools/bbtools/ (accessed on 28 June 2022)