whatshap/whatshap

Bayesian haplotype-based genetic polymorphism discovery and genotyping.

Clair3 - Symphonizing pileup and full-alignment for deep learning-based long-read variant calling

DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data.

Long read based human genomic structural variation detection with cuteSV

SPAdes Genome Assembler

Graph-based alignment (Hierarchical Graph FM index)

Structural variation caller using third generation sequencing

Telomere-to-telomere assembly of accurate long reads (PacBio HiFi, Oxford Nanopore Duplex, HERRO corrected Oxford Nanopore Simplex) and Oxford Nanopore ultra-long reads.

DELLY2: Structural variant discovery by integrated paired-end and split-read analysis