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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.
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.
