2,111 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
RowHammer: Reliability Analysis and Security Implications
As process technology scales down to smaller dimensions, DRAM chips become
more vulnerable to disturbance, a phenomenon in which different DRAM cells
interfere with each other's operation. For the first time in academic
literature, our ISCA paper exposes the existence of disturbance errors in
commodity DRAM chips that are sold and used today. We show that repeatedly
reading from the same address could corrupt data in nearby addresses. More
specifically: When a DRAM row is opened (i.e., activated) and closed (i.e.,
precharged) repeatedly (i.e., hammered), it can induce disturbance errors in
adjacent DRAM rows. This failure mode is popularly called RowHammer. We tested
129 DRAM modules manufactured within the past six years (2008-2014) and found
110 of them to exhibit RowHammer disturbance errors, the earliest of which
dates back to 2010. In particular, all modules from the past two years
(2012-2013) were vulnerable, which implies that the errors are a recent
phenomenon affecting more advanced generations of process technology.
Importantly, disturbance errors pose an easily-exploitable security threat
since they are a breach of memory protection, wherein accesses to one page
(mapped to one row) modifies the data stored in another page (mapped to an
adjacent row).Comment: This is the summary of the paper titled "Flipping Bits in Memory
Without Accessing Them: An Experimental Study of DRAM Disturbance Errors"
which appeared in ISCA in June 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
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