cgroza/GraffiTE

Extensive de-novo TE Annotator

Bayesian haplotype-based genetic polymorphism discovery and genotyping.

Long read based human genomic structural variation detection with cuteSV

Structural variation caller using third generation sequencing

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

A package for including transposable elements in differential enrichment analysis of sequencing datasets.

tools for working with genome variation graphs

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

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