Instruct: Identify the main category of Biorxiv papers based on the titles and abstracts
Query: Atria: An Ultra-fast and Accurate Trimmer for Adapter and Quality Trimming BackgroundAs Next Generation Sequencing takes a dominant role in terms of output capacity and sequence length, adapters attached to the reads and low-quality bases hinder the performance of downstream analysis directly and implicitly, such as producing false-positive single nucleotide polymorphisms (SNP), and generating fragmented assemblies. A fast trimming algorithm is in demand to remove adapters precisely, especially in read tails with relatively low quality.

FindingsWe present a trimming program named Atria. Atria matches the adapters in paired reads and finds possible overlapped regions with a super-fast and carefully designed byte-based matching algorithm (O(n) time with O(1) space). Atria also implements multi-threading in both sequence processing and file compression and supports single-end reads.

ConclusionsAtria performs favorably in various trimming and runtime benchmarks of both simulated and real data with other cutting-edge trimmers. We also provide an ultra-fast and lightweight byte-based matching algorithm. The algorithm can be used in a broad range of short-sequence matching applications, such as primer search and seed scanning before alignment.

Availability & ImplementationThe Atria executables, source code, and benchmark scripts are available at https://github.com/cihga39871/Atria under the MIT license.
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The categories of this paper are: neuroscience
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The categories of this paper are: cognition
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The categories of this paper are: paleontology
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The categories of this paper are: ecology
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The categories of this paper are: education
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The categories of this paper are: physiology
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The categories of this paper are: biology
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The categories of this paper are: behavior
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The categories of this paper are: cancer
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The categories of this paper are: scientific
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The categories of this paper are: genomics
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The categories of this paper are: microbiology
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The categories of this paper are: developmental
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The categories of this paper are: pathology