https://github.com/hgsvc

A collection of workflows and software tools for variant calling and annotation, used in the generation and analysis of 65 HGSVC genomes (Logdson et al., doi: 10.1101/2024.09.24.614721)

https://github.com/eblerjana/pangenie

PanGenie is a genotyper for various types of genetic variants (such as SNPs, indels and structural variants) represented in a pangenome graph. Genotypes are computed based on read k-mer counts and a panel of known haplotypes.

https://github.com/ptrebert/project-diploid-assembly

The Phased Genome Assembly using Strand-seq (PGAS) pipeline is an end-to-end Snakemake workflow that starts from raw sequencing reads and produces fully phased assemblies. PGAS employs state-of-the-art tools for assembly, phasing and quality control, and can easily be deployed on high-performance computing environments for maximal throughput. PGAS is continuously updated to keep pace with technological progress, currently focusing on PacBio HiFi as default long-read technology, and scheduled to support hybrid assemblies combining PacBio HiFi and ONT Ultra-Long in the near future.

https://github.com/EichlerLab/pav

The Phased Assembly Variant (PAV) tool identifies structural variants (SVs), point mutations, and indels based on a direct analysis of genome assemblies as opposed to read-based detection . Both phased and unphased assemblies are supported. PAV introduces algorithms to improve inversion sensitivity and to reduce false calls produced by redundantly aligned bases.

https://github.com/mills-lab/PALMER

PALMER detects non-reference MEI events (LINE, Alu, SVA, and HERVK) and other insertions by using the indexed reference-aligned BAM/CRAM files from long-read technology as inputs.

https://github.com/ChaissonLab/LRA

LRA is alignment software optimized for structural variant discovery from long reads and assemblies.