Instruct: Identify the main and secondary category of Arxiv papers based on the titles and abstracts
Query: Read Mapping Near Non-Volatile Memory   DNA sequencing is the physical/biochemical process of identifying the
location of the four bases (Adenine, Guanine, Cytosine, Thymine) in a DNA
strand. As semiconductor technology revolutionized computing, modern DNA
sequencing technology (termed Next Generation Sequencing, NGS)revolutionized
genomic research. As a result, modern NGS platforms can sequence hundreds of
millions of short DNA fragments in parallel. The sequenced DNA fragments,
representing the output of NGS platforms, are termed reads. Besides genomic
variations, NGS imperfections induce noise in reads. Mapping each read to (the
most similar portion of) a reference genome of the same species, i.e., read
mapping, is a common critical first step in a diverse set of emerging
bioinformatics applications. Mapping represents a search-heavy memory-intensive
similarity matching problem, therefore, can greatly benefit from near-memory
processing. Intuition suggests using fast associative search enabled by Ternary
Content Addressable Memory (TCAM) by construction. However, the excessive
energy consumption and lack of support for similarity matching (under NGS and
genomic variation induced noise) renders direct application of TCAM infeasible,
irrespective of volatility, where only non-volatile TCAM can accommodate the
large memory footprint in an area-efficient way. This paper introduces GeNVoM,
a scalable, energy-efficient and high-throughput solution. Instead of
optimizing an algorithm developed for general-purpose computers or GPUs, GeNVoM
rethinks the algorithm and non-volatile TCAM-based accelerator design together
from the ground up. Thereby GeNVoM can improve the throughput by up to 113.5
times (3.6); the energy consumption, by up to 210.9 times (1.36), when compared
to a GPU (accelerator) baseline, which represents one of the highest-throughput
implementations known.

19
The categories of this paper are: eess
5
The categories of this paper are: gr-qc
34
The categories of this paper are: chem-ph
20
The categories of this paper are: acc-phys
32
The categories of this paper are: atom-ph
31
The categories of this paper are: ao-sci
2
The categories of this paper are: math
30
The categories of this paper are: q-alg
4
The categories of this paper are: cond-mat
10
The categories of this paper are: q-bio
28
The categories of this paper are: alg-geom
36
The categories of this paper are: cmp-lg
23
The categories of this paper are: solv-int
16
The categories of this paper are: stat
37
The categories of this paper are: supr-con
29
The categories of this paper are: funct-an