Resequencing, especially with human samples, is one of the most popular applications of next-generation sequencing. It is used to determine the genomic variations of a sample in relation to a common reference sequence. The generated sequence is aligned to the reference sequence and mined for SNPs and CNVs as well as genomic rearrangements and indels.
This application benefits primarily from generating as much sequence as possible with the smallest budget possible. Longer reads can definitely be beneficial, but the total genomic output (in terms of pure number of bases covered) is more important. Therefore, the flagship platforms from the more established providers tend to be used most heavily in this space.
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