SVPipelinesRanking

We analyzed the performance of 53 pipelines, incorporating five aligners (LRA, minimap2, NGMLR, pbmm2, winnowmap) and twelve callers (cuteSV, cuteSV2, DeBreak, DELLY, pbsv, Picky, NanoSV, NanoVar, Sniffles, Sniffles2, SVIM, SVision). Our evaluation covered various datasets, including simulated and multiple real sample datasets, focusing on metrics like F1 score, precision, recall, length deviation, breakpoint accuracy, and Mendelian error rate (MIER).

After conducting thorough evaluations across different scenarios, we compiled a performance ranking of these 53 pipelines.

If you find our work useful, please cite: Liu, Z., Xie, Z. & Li, M. Comprehensive and deep evaluation of structural variation detection pipelines with third-generation sequencing data. Genome Biol 25, 188 (2024). https://doi.org/10.1186/s13059-024-03324-5