Steven Salzberg

Hybrid assembly of the large and highly repetitive genome of Aegilops tauschii, a progenitor of bread wheat, with the mega-reads algorithm

The paper introduces a hybrid assembly method using long reads and short accurate reads to improve genome contiguity for a highly repetitive plant genome.

HISAT: Hierarchical Indexing for Spliced Alignment of Transcripts

HISAT is a fast and accurate RNA-seq aligner using hierarchical indexing, achieving 50x speed improvement over TopHat2 with comparable accuracy.

Faster sequence alignment through GPU-accelerated restriction of the seed-and-extend search space

The paper introduces A21, a GPU-accelerated read aligner that improves speed and sensitivity by restricting the seed-and-extend search space using parallel sort and reduction techniques.