Software

Ctyper is a genotyping approach for pangenomes to detect alleles that are shared between a biobank (short-read sequencing) sample and a long-read pangenome for challenging and copy-number variable regions of the genome.
bioconda: ctyper
git: https://github.com/chaissonlab/ctyper
publication: https://www.nature.com/articles/s41588-025-02346-4
author: Walfred Ma

STR and VNTR annotation by motif composition for PacBio and Oxford Nanopore reads, and assemblies. The vamos suite contains two components, one to characterize the repeat motifs in a population using an efficient motif set, a subset of motifs that preserves motif sequence diversity while removing rare motifs, and annotation software that uses wraparound dynamic programming to annotate samples using tandem repeat and motif databases. bioconda: vamos
git: https://github.com/chaissonlab/vamos publication: https://link.springer.com/article/10.1186/s13059-023-03010-y
authors: Jingwen Ren and Bida Gu

Detects microsatellite instability in PacBio HiFi reads.
git: https://github.com/pacificbiosciences/owl/
author: Zev Kronenberg

Software for mapping long reads (PacBio/Oxford Nanopore) or their assemblies to genomes. LRA implements an exact convex gap penalty for biologically meaningful gaps to discover structural variation.
git: https://github.com/chaissonlab/lra
bioconda: lra
publication: https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1009078
author: Jingwen Ren

danbing-tk is a suite of tools to construct locus-specific de Bruijn graphs on tandem repeat loci from pangenomes (repeat-pangenome graphs), and to map short reads to the graphs. Length and motif variation can be inferred from alignment depth.
git: https://github.com/chaissonlab/danbing-tk
publications: https://genome.cshlp.org/content/33/4/511.short, https://www.nature.com/articles/s41467-021-24378-0
author: Tony Tsung-Yu Lu