Journal: iScience

Article Title: Systematic benchmarking of tools for structural variation detection using short- and long-read sequencing data in pigs

doi: 10.1016/j.isci.2025.111983

Figure Lengend Snippet: Characterizations of structural variation (SV) callsets using different types of sequencing platforms, reads aligners, and SV callers (A) the number of SVs in each callset. (B) the Jaccard similarity between different callsets in Asian wild boar. The error bars in (A) indicate the standard deviation in the five pig breeds. SVs using Hi-C data were exclusively from the EagleC callset. The two assembly-based callers in (A) are marked by bold italic labels. The callsets in (B) were named as “platform_caller_aligner”. The average clustering method was used to order the callsets. Hi-C: high-throughput chromosome conformation capture; WGS: Illumina whole genome resequencing; HiFi: Pacbio circular consensus sequencing high-fidelity; ONT: Oxford Nanopore technology; DEL: deletion; INS: insertion; INV: inversion; DUP: duplication; TRA: translocation.

Article Snippet: The widely used next-generation sequencing (NGS) platforms, like Illumina whole genome resequencing (WGS), are advantageous on base-level resolution but short on DNA read length, which incurs the inability to accommodate both breakpoints of large and complex SVs.

Techniques: Sequencing, Standard Deviation, Hi-C, High Throughput Screening Assay, Translocation Assay

Journal: iScience

Article Title: Systematic benchmarking of tools for structural variation detection using short- and long-read sequencing data in pigs

doi: 10.1016/j.isci.2025.111983

Figure Lengend Snippet: Precision, recall, and F1 score of structural variation (SV) detection for all SV calling programs capitalizing on three different sequencing platforms Each point is the average value of five pig breeds. The two assembly-based callers are marked by bold italic labels. Total SVs (Total), insertions (INS), and deletions (DEL) were separately assessed. The LUMPY tool cannot detect INS. WGS: Illumina whole genome resequencing; HiFi: Pacbio circular consensus sequencing high-fidelity; ONT: Oxford Nanopore technology.

Article Snippet: The widely used next-generation sequencing (NGS) platforms, like Illumina whole genome resequencing (WGS), are advantageous on base-level resolution but short on DNA read length, which incurs the inability to accommodate both breakpoints of large and complex SVs.

Techniques: Sequencing

Journal: iScience

Article Title: Systematic benchmarking of tools for structural variation detection using short- and long-read sequencing data in pigs

doi: 10.1016/j.isci.2025.111983

Figure Lengend Snippet: Precision and recall of total structural variations detection in regions with different complexities, regions with varying linkage disequilibrium (LD) extents, and regions with runs of homozygosity (ROH) segments or not (unROH) (A) Regions with different complexities. (B) Regions with varying LD extents. (C) Regions with or without ROH. Each point is the average value of five pig breeds. Complex regions include long (LINE) and short (SINE) interspersed nuclear elements, simple repeats, and high and low GC contents regions on chromosome 1. Other indicates regions outside interspersed repeats and low complexity DNA sequences areas on chromosome 1. LD extent is assessed by r 2 . WGS: Illumina whole genome resequencing; HiFi: PacBio circular consensus sequencing high-fidelity; ONT: Oxford Nanopore technology.

Article Snippet: The widely used next-generation sequencing (NGS) platforms, like Illumina whole genome resequencing (WGS), are advantageous on base-level resolution but short on DNA read length, which incurs the inability to accommodate both breakpoints of large and complex SVs.

Techniques: Sequencing