Instruct: Identify the main category of Biorxiv papers based on the titles and abstracts
Query: Accelerating long-read analysis on modern CPUs Long read sequencing is now routinely used at scale for genomics and transcriptomics applications. Mapping of long reads or a draft genome assembly to a reference sequence is often one of the most time consuming steps in these applications. Here, we present techniques to accelerate minimap2, a widely used software for mapping. We present multiple optimizations using SIMD parallelization, efficient cache utilization and a learned index data structure to accelerate its three main computational modules, i.e., seeding, chaining and pairwise sequence alignment. These result in reduction of end-to-end mapping time of minimap2 by up to 1.8 x while maintaining identical output.
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The categories of this paper are: and
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The categories of this paper are: zoology
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The categories of this paper are: synthetic
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The categories of this paper are: paleontology
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The categories of this paper are: biophysics
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The categories of this paper are: systems
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The categories of this paper are: cognition
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The categories of this paper are: physiology
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The categories of this paper are: genetics
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The categories of this paper are: bioinformatics
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The categories of this paper are: toxicology
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The categories of this paper are: scientific
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The categories of this paper are: plant
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The categories of this paper are: ecology
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The categories of this paper are: neuroscience
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The categories of this paper are: animal