1,659 research outputs found
Nanopore Sequencing Technology and Tools for Genome Assembly: Computational Analysis of the Current State, Bottlenecks and Future Directions
Nanopore sequencing technology has the potential to render other sequencing
technologies obsolete with its ability to generate long reads and provide
portability. However, high error rates of the technology pose a challenge while
generating accurate genome assemblies. The tools used for nanopore sequence
analysis are of critical importance as they should overcome the high error
rates of the technology. Our goal in this work is to comprehensively analyze
current publicly available tools for nanopore sequence analysis to understand
their advantages, disadvantages, and performance bottlenecks. It is important
to understand where the current tools do not perform well to develop better
tools. To this end, we 1) analyze the multiple steps and the associated tools
in the genome assembly pipeline using nanopore sequence data, and 2) provide
guidelines for determining the appropriate tools for each step. We analyze
various combinations of different tools and expose the tradeoffs between
accuracy, performance, memory usage and scalability. We conclude that our
observations can guide researchers and practitioners in making conscious and
effective choices for each step of the genome assembly pipeline using nanopore
sequence data. Also, with the help of bottlenecks we have found, developers can
improve the current tools or build new ones that are both accurate and fast, in
order to overcome the high error rates of the nanopore sequencing technology.Comment: To appear in Briefings in Bioinformatics (BIB), 201
Security Analysis of the Silver Bullet Technique for RowHammer Prevention
The purpose of this document is to study the security properties of the
Silver Bullet algorithm against worst-case RowHammer attacks. We mathematically
demonstrate that Silver Bullet, when properly configured and implemented in a
DRAM chip, can securely prevent RowHammer attacks. The demonstration focuses on
the most representative implementation of Silver Bullet, the patent claiming
many implementation possibilities not covered in this demonstration. Our study
concludes that Silver Bullet is a promising RowHammer prevention mechanism that
can be configured to operate securely against RowHammer attacks at various
efficiency-area tradeoff points, supporting relatively small hammer count
values (e.g., 1000) and Silver Bullet table sizes (e.g., 1.06KB).Comment: 40 page
FastRemap: A Tool for Quickly Remapping Reads between Genome Assemblies
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 variety of tools, e.g., the commonly-used CrossMap
tool. With the explosion of available genomic data sets and references,
high-performance remapping tools will be even more important for keeping up
with the computational demands of genome assembly and analysis.
We provide FastRemap, a fast and efficient tool for remapping reads between
genome assemblies. FastRemap provides up to a 7.82 speedup
(6.47, on average) and uses as low as 61.7% (80.7%, on average) of the
peak memory consumption compared to the state-of-the-art remapping tool,
CrossMap.
FastRemap is written in C++. The source code and user manual are freely
available at: github.com/CMU-SAFARI/FastRemap. Docker image available at:
https://hub.docker.com/r/alkanlab/fast. Also available in Bioconda at:
https://anaconda.org/bioconda/fastremap-bio.Comment: FastRemap is open source and all scripts needed to replicate the
results in this paper can be found at https://github.com/CMU-SAFARI/FastRema
- …