73 citations · 285 across the 25 of their papers we have counts for
7 papers · 1 filter
FastRemap: A Tool for Quickly Remapping Reads between Genome Assemblies
Jeremie S. Kim, Can Firtina, Meryem Banu Cavlak +3
A genome read data set can be quickly and efficiently remapped from one reference to another similar reference (e.g., between two reference versions or two similar species) using a…
BLEND: A Fast, Memory-Efficient, and Accurate Mechanism to Find Fuzzy Seed Matches in Genome Analysis
Can Firtina, Jisung Park, Mohammed Alser +8
Generating the hash values of short subsequences, called seeds, enables quickly identifying similarities between genomic sequences by matching seeds with a single lookup of their h…
AirLift: A Fast and Comprehensive Technique for Remapping Alignments between Reference Genomes
Jeremie S. Kim, Can Firtina, Meryem Banu Cavlak +5
AirLift is the first read remapping tool that enables users to quickly and comprehensively map a read set, that had been previously mapped to one reference genome, to another simil…
Apollo: A Sequencing-Technology-Independent, Scalable, and Accurate Assembly Polishing Algorithm
Can Firtina, Jeremie S. Kim, Mohammed Alser +4
Long reads produced by third-generation sequencing technologies are used to construct an assembly (i.e., the subject's genome), which is further used in downstream genome analysis.…
GRIM-Filter: Fast Seed Location Filtering in DNA Read Mapping Using Processing-in-Memory Technologies
Jeremie S. Kim, Damla Senol Cali, Hongyi Xin +7
Motivation: Seed location filtering is critical in DNA read mapping, a process where billions of DNA fragments (reads) sampled from a donor are mapped onto a reference genome to id…
Nanopore Sequencing Technology and Tools for Genome Assembly: Computational Analysis of the Current State, Bottlenecks and Future Directions
Damla Senol Cali, Jeremie S. Kim, Saugata Ghose +2
Nanopore sequencing technology has the potential to render other sequencing technologies obsolete with its ability to generate long reads and provide portability. However, high err…