Table 2.

Comparison of various NGS technique and primary analysis tools.

NGS techniques	Study aim(s)	Data size per sample	Tool(s) used	Reference
WGS	De novo assembly	~90 GB	Velvet, SOAPdenovo	Zerbino and Birney, 2008; Luo et al., 2012
WES	Protein-coding variant identification	~5–6 GB	Edico DRAGEN, GATK, Samtools	Li et al., 2009; McKenna et al., 2010; Edico Genome, 2018
RNA-seq	Gene expression, novel isoform discovery	~3–4 GB	DESeq, Cufflinks	Anders and Huber, 2010; Trapnell et al., 2012
ChIP-seq	Protein–DNA interaction study, i.e., identification of histone marks and transcription factor binding sites	~1–2 GB	QuEST, MACS	Valouev et al., 2008; Liu, 2014
Bisulfite-seq	DNA methylation sites identification	~1–2 GB	BS Seeker	Chen et al., 2010