Movi indexes

Movi (GitHub repo) is an efficient and scalable approach for indexing and querying pangenomes. It uses the move structure of Nishimoto and Tabei as its core, cache-efficient index structure.

The indexes below are separator-aware, reverse-complement-aware pangenome indexes for Movi 2. They are built in Movi’s regular-thresholds mode (mode 6) and include threshold information, so they support the full range of Movi 2 queries: pseudo-matching lengths (--pml), Ziv–Lempel matching lengths (--zml), --count, k-mer presence/counts (--kmer), maximal exact matches (--mem), and — using the shipped null model — read --classify and --filter. A % separator is placed after every record and between each record’s forward and reverse-complement copy, so matches never spuriously extend across a record (contig) boundary.

Each index was built on JHU’s Rockfish cluster. The two larger indexes (HPRC Release 2 and OpenHGL) are the first Movi indexes whose reference length exceeds 2⁴⁰ bp; they use a wide (6-byte) threshold format produced by an updated build path. The published indexes are queryable by stock Movi 2 — the wide-threshold change is build-time only and does not alter the on-disk index format.

Every index ships a signed test-witness.json recording the results of a corner-case query-mode test suite (separator non-extension, reverse-complement symmetry, illegal/non-ACGT character handling, positive-vs-null separation, and cross-mode consistency) run against that exact index.movi; the witness pins the index’s SHA-256 and the Movi commit, and carries a self-verifying self_sha256. All three indexes passed with zero failures.

The following table lists each complete .tar.gz archive, then the individual component files contained in that archive.

The .seqdict.json file maps each index position back to its source record (sample, contig, and orientation). The movi-index.yaml sidecar records the index header (mode, reference length, run count) and build provenance.

Corresponding S3 URLs can be obtained by replacing the https://genome-idx.s3.amazonaws.com/ prefix with s3://genome-idx/.

Movi is the work of Mohsen Zakeri, Nathaniel Brown, Travis Gagie and Ben Langmead.