ArticleiScience2024
Building a pangenome alignment index via recursive prefix-free parsing.
Article in iScience, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 5 papers.
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Who cites it
5 citing papers in PubMed.
- Building genomic data structures from compressed representations using prefix-free parsing.Genome research · 2026Review
- Partitioned multi-MUM finding for scalable pangenomics with MumemtoM.Genome research · 2026Article
- Prefix-free parsing for merging big BWTs.International Symposium on String Processing and Information Retrieval : SPIRE ... : proceedings. SPIRE (Symposium) · 2026Article
- Mumemto: efficient maximal matching across pangenomes.Genome biology · 2025Article
- Partitioned Multi-MUM finding for scalable pangenomics.bioRxiv : the preprint server for biology · 2025Article
Corrections and comments
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Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Pangenomics alignment offers a solution to reduce bias in biomedical research. Traditionally, short-read aligners like Bowtie and BWA indexed a single reference genome to find approximate alignments. These methods, limited by linear-memory requirements, can only index a few genomes. Emerging pangenome aligners, such as VG, Giraffe, and Moni, address this by indexing more genomes. VG and Giraffe use a variation graph, while Moni indexes sequences accounting for repetition using prefix-free parsing to build a dictionary and parse. The main challenge is the parse's size, which becomes significantly larger than the dictionary. To scale Moni, we propose removing the parse from the construction of the run-length encoded BWT (RLBWT), suffix array, and Longest Common Prefix (LCP) by applying prefix-free parsing recursively. This approach improves construction time and memory requirements, enabling efficient construction of RLBWT, suffix array, and LCP for large pangenomes, such as those from the Human Pangenome Reference Consortium.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.