Jamshed Khan

kache-hash: A dynamic, concurrent, and cache-efficient hash table for streaming k-mer operations

kache-hash improves k-mer hash table performance for genomic analysis by leveraging minimizers and cache efficiency, achieving faster builds and queries across multiple datasets.

Alevin-fry-atac enables rapid and memory frugal mapping of single-cell ATAC-seq data using virtual colors for accurate genomic pseudoalignment

Alevin-fry-atac provides a fast, memory-efficient method for single-cell ATAC-seq data processing with high accuracy compared to existing tools.

Faster and Scalable Parallel External-Memory Construction ofColored Compacted de Bruijn Graphs with Cuttlefish 3

Cuttlefish 3 is a parallel external-memory algorithm for constructing colored compacted de Bruijn graphs, achieving significant speedup over existing tools.

Fulgor: A fast and compact k-mer index for large-scale matching and color queries

Fulgor is a compact k-mer index for efficient sequence matching and color queries, outperforming existing methods in space and speed.

Spectrum preserving tilings enable sparse and modular reference indexing

The paper introduces a method to reduce the space required for reference indexing by using spectrum preserving tilings and sampling schemes, achieving significant space savings with minimal query slowdown.

Scalable, ultra-fast, and low-memory construction of compacted de Bruijn graphs with Cuttlefish 2

The paper introduces Cuttlefish 2, a tool that significantly speeds up and reduces memory usage for constructing compacted de Bruijn graphs from large genomic datasets.

Cuttlefish: Fast, parallel, and low-memory compaction of de Bruijn graphs from large-scale genome collections

Cuttlefish constructs compacted de Bruijn graphs from genome collections efficiently, outperforming existing tools in speed and memory usage.

An Incrementally Updatable and Scalable System for Large-Scale Sequence Search using LSM Trees

The paper introduces an updatable and scalable exact sequence-search index based on Mantis, demonstrating its efficiency and scalability over large datasets.