Open-source software

A compressed, queryable index over pangenome graphs containing thousands of haplotype paths. pansift keeps the full graph + path set in memory at roughly 18 bytes per node for vertebrate-scale graphs, and supports sub-millisecond path queries needed for graph-coordinate variant projection and graph-aware read alignment. Used internally as the index backend for graphmap2 and svhound.

A structural-variant caller that operates directly on aligned reads in graph space (GAF input) and reports variants relative to the graph rather than to a single linear reference. Designed for nested, overlapping, and repeat-embedded variation that linear-reference callers either miss or merge. Outputs a graph-coordinate VCF (vg-style) with optional projection to any chosen reference path for compatibility with downstream tools.

An interactive visualisation tool for inspecting structural variants in their pangenome graph context. loomvar reads graph-coordinate VCFs (from svhound or vg deconstruct) plus the underlying graph and produces ribbon and bandage-style views that include adjacent path-support tracks. Browser-based, served from a single binary, no upload required — all rendering is local.

A targeted local re-assembly tool that closes gaps in long-read assemblies caused by Nanopore signal dropouts (homopolymer runs, low-complexity tracts, and certain methylated motifs). ribbon-bridge is read-set agnostic — it works with PacBio HiFi rescue reads, ultra-long Nanopore, or Sanger sequencing of PCR products — and outputs patched contigs with provenance tags showing where each base came from.

A long-read aligner designed from the ground up for pangenome graphs rather than linear references. graphmap2 produces GAF output, scales to chromosome-scale graphs with thousands of paths, and is the default aligner used by the lab’s downstream callers. Multi-threaded, low memory footprint, and benchmarked against minigraph and GraphAligner on the lab’s reproducibility test suite.

A small, fast command-line tool for QC of GAF (graph alignment) files. gafstat reports per-path coverage, secondary-alignment rates, node-traversal entropy, and identity distributions in seconds for whole-chromosome GAFs. Written to be the samtools flagstat of the graph alignment world — no surprises, no dependencies, parseable output.