A few years ago, Tsachy Weissman asked if GBZ files could be compressed further. It turned out zstd compression could reduce their size by ~40%. Since GBZ-base made memory-mapped GBZ unnecessary, it became possible to add further compression to the format.

1/ Excited to share the newest tool in the pangenome MUMiverse: Shredtools! Shredtools enables a user to navigate the pangenome coordinate system with multi-MUMs. More in the thread🧵 Code: github.com/vikshiv/shredtools Interactive tool for querying HPRC assemblies: vikshiv.github.io/shredtools

Navigating the pangenome coordinate system with Shredtools

Existing notions of pangenome coordinates rely on hard-to-compute multiple sequence alignments. On the other hand, pangenome-wide exact unique matches (multi-MUMs) can be computed efficiently, and rep...

biorxiv.org

Finally got the GBZ-base / GAF-base preprint out. This started as a side project a few years ago, but it eventually got a bit more serious. 1/

GBZ-base and GAF-base: Indexed pangenome file formats

Motivation: Existing pangenome file formats are designed for batch processing. Graphs must be loaded into memory, and alignment files must be read sequentially. Indexed file formats that can be used d...

biorxiv.org

Movi 2 has appeared (as an advance article) in Bioinformatics 🧬 Faster, leaner pangenome queries — half the memory of Movi 1, ~30% faster. Paper: academic.oup.com/bioinformati... Code: github.com/mohsenzakeri/Movi (1/6)

Inspired by this, I decided to try if Claude could convert my GAF sorting code from C++ to Rust. It's basically external memory multi-way mergesort with integer keys, opaque values, special handling for header lines, and compressed temporary files. 1/

Rob Patro@robp.bsky.social · 6mo ago

I’ve written a post about my recent experiences (successes) with AI coding models; the experiences that caused me to re-evaluate my initial judgements, the surprise I had at what can be accomplished, & some fears I have about these tools. Discussion welcome! combine-lab.github.io/blog/2026/02...

Our latest vg release introduces GBZ v2 with better compression for sequences. I originally assumed that the total sequence length in a pangenome graph would be similar to the size of the genome. This does not hold in the full HPRC graphs due to unaligned centromeres.

Looking for a postdoc to build my new lab at TGen (Phoenix, AZ) focused on pangenome methods for cancer and complex disease. Full stack — from pangenome assembly and compression to association studies and somatic variant discovery. Reach out if interested! guarracinolab.github.io#join

Guarracino Lab | Pangenome Research

We develop methods to build and analyze pangenomes, with applications in cancer and complex disease. Translational Genomics Research Institute, Phoenix, AZ.

guarracinolab.github.io

I am looking for a postdoc to develop high-performance algorithms in computational genomics. Email or DM me if interested. For more information, see hlilab.github.io/vacancies. RTs appreciated!

First time seeing this and it is really great! abseil.io/fast/hints.h...

VG will soon start adding headers to the GAF files it generates. The specifics are still uncertain, but if you maintain a GAF parser, it may be a good idea to skip lines starting with "@". Here is a draft specification for the vg flavor of GAF.

1/6 Movi 2 is here: faster and more space-efficient for pangenome queries. Its fastest mode uses half the memory of Movi 1 while running ~30% faster. github.com/mohsenzakeri...

GitHub - mohsenzakeri/Movi: Fast, Cache-Efficient, and Scalable Queries on Pangenomes

Fast, Cache-Efficient, and Scalable Queries on Pangenomes - mohsenzakeri/Movi

github.com

For the weekend crowd. I'm hiring a postdoc! If you're interested in algorithms, data structures and high-dimensional inference, and if you want to invent new methods for genomics and implement them in high-performance, robust and easy-to-use software, do I have a lab for you; ours!

Rob Patro@robp.bsky.social · 11mo ago

Hi bioinformatics, genomics and CS friends! Please help me spread the word. I'm hiring a postdoc! Come work on cutting edge method development in algorithmic genomics with me and my group at @umdscience.bsky.social! 🖥️🧬

🦒Long read giraffe is out!🦒 Mapping long reads to pangenome graphs is ~10x faster than with GraphAligner, with veeery slightly better mapping accuracy, short variant calling, and SV genotyping than GraphAligner or Minimap2

bioRxiv Bioinfo@biorxiv-bioinfo.bsky.social · 11mo ago

Rapid, accurate long- and short-read mapping to large pangenome graphs with vg Giraffe https://www.biorxiv.org/content/10.1101/2025.09.29.678807v1

We are glad to announce that the next workshop “Data Structures in Bioinformatics” (DSB 2026) will take place in Venice, Italy, on *February 18-19*, 2026. dsb-meeting.github.io/DSB2026/ Book the dates! #DSB26

GBZ-base has been a side project for me for a couple of years. It's basically a GBZ graph stored in SQLite instead of a custom file format. You can convert a GBZ graph to GBZ-base quickly and then extract subgraphs around nodes / reference positions on a laptop. 1/n

GitHub - jltsiren/gbz-base: Prototype for an immutable pangenome graph in SQLite

Prototype for an immutable pangenome graph in SQLite - jltsiren/gbz-base

github.com

Last talk of the day (before posters) "Lossless Pangenome Indexing Using Tag Arrays" presented by Parsa Eskandar! #WABI25

There was a workshop on 25 years of the FM-index and the CSA after SEA. I would have liked to attend, but I had other commitments. The invited speakers were Giovanni Manzini and Roberto Grossi, as the other purpose of the workshop was to present them Festschrifts for their 60th birthdays. 1/6

A new preprint on indexing pangenome graphs using an FM-index of the haplotypes and a tag array. Joint work with Parsa Eskandar and @benedictpaten.bsky.social.

Lossless Pangenome Indexing Using Tag Arrays

Pangenome graphs represent the genomic variation by encoding multiple haplotypes within a unified graph structure. However, efficient and lossless indexing of such structures remains challenging due t...

biorxiv.org

We use personalized references with our Giraffe aligner. Each chromosome is partitioned into a sequence of blocks. We sample the most relevant haplotypes in each block using kmer counts. Mapping to this personalized reference improves variant calling accuracy. www.nature.com/articles/s41...

Personalized pangenome references - Nature Methods

This work introduces a k-mer-based approach to customizing a pangenome reference, making it more relevant to a new sample of interest. This method enhances the accuracy of genotyping small variants an...

nature.com

Coming up soon in vg: faster GAF sorting. The old algorithm was spending too much time parsing and serializing alignments. The new algorithm just deals with blobs and integer keys. With that and some algorithmic improvements, you can now expect to sort 30x short reads in 15-20 minutes on a laptop.