What factors should I consider when planning a next generation sequencing (NGS) experiment?

The main factors to consider when planning a NGS experiment include: 

• Multiplexing options allows multiple samples to be sequenced together in a single sequencing run, using unique barcode sequences to differentiate between samples. Multiplexing increases throughput and reduces per-sample sequencing costs by allowing efficient use of sequencing capacity.
• Depth of sequencing coverage refers to the number of times each base in the genome is sequenced on average. Higher coverage depth provides greater confidence in variant calling, identification of rare mutations, and detection of low-abundance transcripts.
• Length of sequencing reads refers to the number of nucleotides that can be sequenced in a single sequencing cycle. In whole genome sequencing, longer sequencing reads are preferred due to their ability to provide more comprehensive coverage of genomic regions. Short reads are well-suited for applications focused on quantifying the abundance of specific sequences and detecting variants within conserved sequences. 
• Deciding between single-end vs. paired-end sequencing: In single-end sequencing, sequencing is carried only from one end of the DNA fragment, providing sequence information for one end of each fragment. Paired-end sequencing involves sequencing both ends of each DNA fragment, providing paired reads with sequence information from both ends.