When planning time and resources to complete secondary analysis, you must be aware of the sequencing depth of coverage for sample data. It impacts the analysis time per sample. Coverage describes the average number of reads in sequencing that align to, or cover, a known reference sequence. The coverage often determines if a variant exists with a certain degree of confidence at a specific genomic location. Coverage requirements vary by sequencing application. For example, 30x to 60x coverage is common for human WGS applications (Illumina Inc, 2019 July 22). However, the analysis of cancer genomes may require sequencing to a depth of coverage higher than 100x. This depth of coverage is required to achieve the necessary sensitivity and specificity to detect rare, low frequency variants (Griffith, 2015).

Coverage is also a measure of the amount of data per sample. As coverage increases, so does the amount of data per sample. For example, a 50x (coverage) WGS sample contains approximately five times more data than a 10x WGS sample. This sample size means that secondary analysis time increases proportional to the amount of data.