The Sequence Read Archive (SRA) holds petabytes of raw sequencing data, but searching it for a given sequence has long been impractical at scale. This project builds compact, exact, and information-rich indexes that make large-scale sequence search fast and space-efficient.
Most recently, we enabled noise-robust DNA search at SRA scale via local-alignment embeddings with LOCALE (Synk et al., 2026). We introduced Squeakr (Pandey et al., 2017) for fast and compact $k$-mer counting, and the Mantis system (Pandey et al., 2018; Almodaresi et al., 2019) for exact, large-scale sequence search. These build on succinct colored de Bruijn graph representations such as deBGR (Pandey et al., 2017) and Rainbowfish (Almodaresi et al., 2017). We made the search index incrementally updatable (Almodaresi et al., 2022), extended the approach to genomic variant search with VariantStore (Pandey et al., 2021), and scaled colored compacted de Bruijn graph construction to massive datasets with Cuttlefish 3 (Khan et al., 2026). We continue to push toward faster and distributed search: accelerating streaming $k$-mer operations with a dynamic, concurrent, cache-efficient hash table (Khan et al., 2026) and balancing load across distributed genomic indices (Galbraith et al., 2026).
References
2026
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LOCALE: Local-Alignment Embeddings for Noise-Robust DNA Search at SRA Scale
Ryan P. Synk, Prashant Pandey, S. Cenk Sahinalp, and 1 more author
bioRxiv, 2026
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Faster and Scalable Parallel External-Memory Construction of Colored Compacted de Bruijn Graphs with Cuttlefish 3
Jamshed Khan, Laxman Dhulipala, Prashant Pandey, and 1 more author
In International Conference on Research in Computational Molecular Biology 2026, 2026
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kache-hash: A Dynamic, Concurrent, and Cache-Efficient Hash Table for Streaming k-mer Operations
Jamshed Khan, Rob Patro, and Prashant Pandey
bioRxiv, 2026
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Similarity-Based Load-Balancing for Distributed Genomic Indices
Woodward Galbraith, Ilgar Mammadov, Shreyaan Pathak, and 2 more authors
In VLDB 2026 Workshop on Biomedical Data Management Systems (BioDMS), 2026
2022
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An Incrementally Updatable and Scalable System for Large-Scale Sequence Search using the Bentley-Saxe Transformation
Fatemeh Almodaresi, Jamshed Khan, Sergey Madaminov, and 4 more authors
Bioinformatics, 2022
2021
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VariantStore: an index for large-scale genomic variant search
Prashant Pandey, Yinjie Gao, and Carl Kingsford
Genome biology, 2021
2019
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An Efficient, Scalable and Exact Representation of High-Dimensional Color Information Enabled via de Bruijn Graph Search Problem
Fatemeh Almodaresi, Prashant Pandey, Michael Ferdman, and 2 more authors
In Research in Computational Molecular Biology - 23rd Annual International Conference, RECOMB 2019, Washington, DC, USA, May 5-8, 2019, Proceedings, 2019
2018
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RECOMB 2018, Cell Systems 2018 Mantis: A Fast, Small, and Exact Large-Scale Sequence-Search Index
Prashant Pandey, Fatemeh Almodaresi, Michael A. Bender, and 3 more authors
In Research in Computational Molecular Biology - 22nd Annual International Conference, RECOMB 2018, Paris, France, April 21-24, 2018, Proceedings, 2018
2017
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ISMB 2017, BIOINFORMATICS 2017 -
Rainbowfish: A Succinct Colored de Bruijn Graph Representation
Fatemeh Almodaresi, Prashant Pandey, and Rob Patro
In 17th International Workshop on Algorithms in Bioinformatics, WABI 2017, August 21-23, 2017, Boston, MA, USA, 2017