Aquila_stLFR: diploid genome assembly based structural variant calling package for stLFR linked-reads.

ABSTRACT:

Motivation

Identifying structural variants (SVs) is critical in health and disease, however, detecting them remains a challenge. Several linked-read sequencing technologies, including 10X Genomics, TELL-Seq and single tube long fragment read (stLFR), have been recently developed as cost-effective approaches to reconstruct multi-megabase haplotypes (phase blocks) from sequence data of a single sample. These technologies provide an optimal sequencing platform to characterize SVs, though few computational algorithms can utilize them. Thus, we developed Aquila_stLFR, an approach that resolves SVs through haplotype-based assembly of stLFR linked-reads.

Results

Aquila_stLFR first partitions long fragment reads into two haplotype-specific blocks with the assistance of the high-qual

SUBMITTER: Liu YH 

PROVIDER: S-EPMC9710574 | biostudies-literature | 2021

REPOSITORIES: biostudies-literature