4 papers
AutoCSF: Provably Space-Efficient Indexing of Skewed Key-Value Workloads via Filter-Augmented Compressed Static Functions
David Torres Ramos, Vihan Lakshman, Chen Luo +2
We study the problem of building space-efficient, in-memory indexes for massive key-value datasets with highly skewed value distributions. This challenge arises in many data-intens…
GraSSRep: Graph-Based Self-Supervised Learning for Repeat Detection in Metagenomic Assembly
Ali Azizpour, Advait Balaji, Todd J. Treangen +1
Repetitive DNA (repeats) poses significant challenges for accurate and efficient genome assembly and sequence alignment. This is particularly true for metagenomic data, where genom…
Accelerating SARS-CoV-2 low frequency variant calling on ultra deep sequencing datasets
Bryce Kille, Yunxi Liu, Nicolae Sapoval +4
With recent advances in sequencing technology it has become affordable and practical to sequence genomes to very high depth-of-coverage, allowing researchers to discover low-freque…
Fast Processing and Querying of 170TB of Genomics Data via a Repeated And Merged BloOm Filter (RAMBO)
Gaurav Gupta, Minghao Yan, Benjamin Coleman +5
DNA sequencing, especially of microbial genomes and metagenomes, has been at the core of recent research advances in large-scale comparative genomics. The data deluge has resulted…