Tradeoffs in alignment and assembly-based methods for structural variant detection with long-read sequencing data.

ABSTRACT: Long-read sequencing offers long contiguous DNA fragments, facilitating diploid genome assembly and structural variant (SV) detection. Efficient and robust algorithms for SV identification are crucial with increasing data availability. Alignment-based methods, favored for their computational efficiency and lower coverage requirements, are prominent. Alternative approaches, relying solely on available reads for de novo genome assembly and employing assembly-based tools for SV detection via comparison to a reference genome, demand significantly more computational resources. However, the lack of comprehensive benchmarking constrains our comprehension and hampers further algorithm development. Here we systematically compare 14 read alignment-based SV calling methods (including 4 deep learning-

SUBMITTER: Liu YH 

PROVIDER: S-EPMC10951360 | biostudies-literature | 2024 Mar

REPOSITORIES: biostudies-literature