ReadBouncer: precise and scalable adaptive sampling for nanopore sequencing.

ABSTRACT:

Motivation

Nanopore sequencers allow targeted sequencing of interesting nucleotide sequences by rejecting other sequences from individual pores. This feature facilitates the enrichment of low-abundant sequences by depleting overrepresented ones in-silico. Existing tools for adaptive sampling either apply signal alignment, which cannot handle human-sized reference sequences, or apply read mapping in sequence space relying on fast graphical processing units (GPU) base callers for real-time read rejection. Using nanopore long-read mapping tools is also not optimal when mapping shorter reads as usually analyzed in adaptive sampling applications.

Results

Here, we present a new approach for nanopore adaptive sampling that combines fast CPU and GPU base calling with read classifica

SUBMITTER: Ulrich JU 

PROVIDER: S-EPMC9235500 | biostudies-literature | 2022 Jun

REPOSITORIES: biostudies-literature