Instruct: Identify the main and secondary category of Arxiv papers based on the titles and abstracts
Query: A Memory-Efficient FM-Index Constructor for Next-Generation Sequencing
  Applications on FPGAs   FM-index is an efficient data structure for string search and is widely used
in next-generation sequencing (NGS) applications such as sequence alignment and
de novo assembly. Recently, FM-indexing is even performed down to the read
level, raising a demand of an efficient algorithm for FM-index construction. In
this work, we propose a hardware-compatible Self-Aided Incremental Indexing
(SAII) algorithm and its hardware architecture. This novel algorithm builds
FM-index with no memory overhead, and the hardware system for realizing the
algorithm can be very compact. Parallel architecture and a special prefetch
controller is designed to enhance computational efficiency. An SAII-based
FM-index constructor is implemented on an Altera Stratix V FPGA board. The
presented constructor can support DNA sequences of sizes up to 131,072-bp,
which is enough for small-scale references and reads obtained from current
major platforms. Because the proposed constructor needs very few hardware
resource, it can be easily integrated into different hardware accelerators
designed for FM-index-based applications.

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The categories of this paper are: atom-ph
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The categories of this paper are: eess
11
The categories of this paper are: hep-lat
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The categories of this paper are: math-ph
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The categories of this paper are: acc-phys
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The categories of this paper are: hep-ex
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The categories of this paper are: cond-mat
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The categories of this paper are: bayes-an
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The categories of this paper are: alg-geom
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The categories of this paper are: hep-th
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The categories of this paper are: chao-dyn
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The categories of this paper are: comp-gas
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The categories of this paper are: patt-sol
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The categories of this paper are: q-fin
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The categories of this paper are: nucl-ex
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The categories of this paper are: physics