S-leaping: an efficient downsampling method for large high-throughput sequencing data.

ABSTRACT:

Motivation

Sequencing coverage is among key determinants considered in the design of omics studies. To help estimate cost-effective sequencing coverage for specific downstream analysis, downsampling, a technique to sample subsets of reads with a specific size, is routinely used. However, as the size of sequencing becomes larger and larger, downsampling becomes computationally challenging.

Results

Here, we developed an approximate downsampling method called s-leaping that was designed to efficiently and accurately process large-size data. We compared the performance of s-leaping with state-of-the-art downsampling methods in a range of practical omics-study downsampling settings and found s-leaping to be up to 39% faster than the second-fastest method, with comparable accuracy

SUBMITTER: Kuwahara H 

PROVIDER: S-EPMC10318387 | biostudies-literature | 2023 Jul

REPOSITORIES: biostudies-literature