Predicting the Number of Bases to Attain Sufficient Coverage in High-Throughput Sequencing Experiments.

ABSTRACT: For many types of high-throughput sequencing experiments, success in downstream analysis depends on attaining sufficient coverage for individual positions in the genome. For example, when identifying single-nucleotide variants de novo, the number of reads supporting a particular variant call determines our confidence in that variant call. If sequenced reads are distributed uniformly along the genome, the coverage of a nucleotide position is easily approximated by a Poisson distribution, with rate equal to average sequencing depth. Unfortunately, as has become well known, high-throughput sequencing data are never uniform. The numerous factors contributing to variation in coverage have resisted attempts at direct modeling and change along with minor adjustments in the underlying technology.

SUBMITTER: Deng C 

PROVIDER: S-EPMC7398442 | biostudies-literature | 2020 Jul

REPOSITORIES: biostudies-literature