research
∙
12/09/2022
TargetCall: Eliminating the Wasted Computation in Basecalling via Pre-Basecalling Filtering
Basecalling is an essential step in nanopore sequencing analysis where t...
share
research
∙
05/12/2022
SeGraM: A Universal Hardware Accelerator for Genomic Sequence-to-Graph and Sequence-to-Sequence Mapping
A critical step of genome sequence analysis is the mapping of sequenced ...
research
∙
03/27/2021
GateKeeper-GPU: Fast and Accurate Pre-Alignment Filtering in Short Read Mapping
At the last step of short read mapping, the candidate locations of the r...
research
∙
09/16/2020
GenASM: A High-Performance, Low-Power Approximate String Matching Acceleration Framework for Genome Sequence Analysis
Genome sequence analysis has enabled significant advancements in medical...
research
∙
07/30/2020
Accelerating Genome Analysis: A Primer on an Ongoing Journey
Genome analysis fundamentally starts with a process known as read mappin...
research
∙
12/18/2019
AirLift: A Fast and Comprehensive Technique for Translating Alignments between Reference Genomes
As genome sequencing tools and techniques improve, researchers are able ...
research
∙
10/20/2019
SneakySnake: A Fast and Accurate Universal Genome Pre-Alignment Filter for CPUs, GPUs, and FPGAs
Motivation: We introduce SneakySnake, a highly parallel and highly accur...
research
∙
02/12/2019
Apollo: A Sequencing-Technology-Independent, Scalable, and Accurate Assembly Polishing Algorithm
A large proportion of the basepairs in the long reads that third-generat...
research
∙
09/18/2018
Shouji: A Fast and Efficient Pre-Alignment Filter for Sequence Alignment
Motivation: The ability to generate massive amounts of sequencing data c...
research
∙
09/18/2018
Shouji: Fast and Efficient Computation of Banded Sequence Alignment
Motivation: The ability to generate massive amounts of sequencing data c...
research
∙
09/18/2018
SLIDER: Fast and Efficient Computation of Banded Sequence Alignment
Motivation: The ability to generate massive amounts of sequencing data c...
research
∙
06/30/2018
Fast Characterization of Segmental Duplications in Genome Assemblies
Segmental duplications (SDs), or low-copy repeats (LCR), are segments of...
research
∙
04/06/2016