Demonstrating the utility of flexible sequence queries against indexed short reads with FlexTyper.

ABSTRACT: Across the life sciences, processing next generation sequencing data commonly relies upon a computationally expensive process where reads are mapped onto a reference sequence. Prior to such processing, however, there is a vast amount of information that can be ascertained from the reads, potentially obviating the need for processing, or allowing optimized mapping approaches to be deployed. Here, we present a method termed FlexTyper which facilitates a "reverse mapping" approach in which high throughput sequence queries, in the form of k-mer searches, are run against indexed short-read datasets in order to extract useful information. This reverse mapping approach enables the rapid counting of target sequences of interest. We demonstrate FlexTyper's utility for recovering depth of coverage,

SUBMITTER: Richmond PA 

PROVIDER: S-EPMC8016220 | biostudies-literature | 2021 Mar

REPOSITORIES: biostudies-literature