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Accurate short-read alignment through r-index-based pangenome indexing.

Rahul Varki¹, Massimiliano Rossi¹, Eddie Ferro¹

¹Department of Computer and Information Science and Engineering, University of Florida, Gainesville, Florida 32611, USA.

Genome Research

|June 12, 2025

Summary

Moni-align is a new tool that improves short-read alignment by using pangenomes instead of linear references. This reduces errors caused by genetic variations, enhancing mapping accuracy for genomic studies.

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Area of Science:

Genomics
Bioinformatics
Computational Biology

Background:

Linear reference genomes can lead to mapping inaccuracies (reference bias) due to uncaptured genetic variations.
Pangenomes, collections of diverse genomes, are emerging as a solution to mitigate reference bias in genomic analysis.

Purpose of the Study:

Introduce Moni-align, the first short-read pangenome aligner.
Evaluate Moni-align's performance against existing pangenome alignment tools.

Main Methods:

Developed Moni-align utilizing the r-index for efficient indexing of genome collections.
Implemented a seed-and-extend alignment strategy using maximal exact matches derived from the r-index.
Tested Moni-align with both simulated and real short-read sequencing data.

Main Results:

Moni-align demonstrates alignment accuracy comparable to leading pangenome aligners like vg map and vg giraffe.
The r-index enables efficient indexing of pangenomes in O(r)-space.

Conclusions:

Moni-align provides a robust foundation for pangenome alignment, offering improved accuracy over linear references.
Current limitations include computational constraints for large-scale pangenomes, with potential for future optimization.