A compressive seeding algorithm in conjunction with reordering-based compression.

ABSTRACT:

Motivation

Seeding is a rate-limiting stage in sequence alignment for next-generation sequencing reads. The existing optimization algorithms typically utilize hardware and machine-learning techniques to accelerate seeding. However, an efficient solution provided by professional next-generation sequencing compressors has been largely overlooked by far. In addition to achieving remarkable compression ratios by reordering reads, these compressors provide valuable insights for downstream alignment that reveal the repetitive computations accounting for more than 50% of seeding procedure in commonly used short read aligner BWA-MEM at typical sequencing coverage. Nevertheless, the exploited redundancy information is not fully realized or utilized.

Results

In this study, we present

SUBMITTER: Ji F 

PROVIDER: S-EPMC10955252 | biostudies-literature | 2024 Mar

REPOSITORIES: biostudies-literature