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HiFiAdapterFilt, a memory efficient read processing pipeline, prevents occurrence of adapter sequence in PacBio HiFi reads and their negative impacts on genome assembly.

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  • Additional Information
    • Source:
      Publisher: BioMed Central Country of Publication: England NLM ID: 100965258 Publication Model: Electronic Cited Medium: Internet ISSN: 1471-2164 (Electronic) Linking ISSN: 14712164 NLM ISO Abbreviation: BMC Genomics Subsets: MEDLINE
    • Publication Information:
      Original Publication: London : BioMed Central, [2000-
    • Subject Terms:
      High-Throughput Nucleotide Sequencing* ; Software*; Gene Library ; Sequence Analysis, DNA
    • Abstract:
      Background: Pacific Biosciences HiFi read technology is currently the industry standard for high accuracy long-read sequencing that has been widely adopted by large sequencing and assembly initiatives for generation of de novo assemblies in non-model organisms. Though adapter contamination filtering is routine in traditional short-read analysis pipelines, it has not been widely adopted for HiFi workflows.
      Results: Analysis of 55 publicly available HiFi datasets revealed that a read-sanitation step to remove sequence artifacts derived from PacBio library preparation from read pools is necessary as adapter sequences can be erroneously integrated into assemblies.
      Conclusions: Here we describe the nature of adapter contaminated reads, their consequences in assembly, and present HiFiAdapterFilt, a simple and memory efficient solution for removing adapter contaminated reads prior to assembly.
      (© 2022. The Author(s).)
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    • Grant Information:
      2040-22430-027-00-D agricultural research service; 0500-00093-001-00-D Oak Ridge Institute for Science and Education
    • Contributed Indexing:
      Keywords: Adapter; Circular consensus sequencing; PacBio HiFi; Sequence data filtering
    • Publication Date:
      Date Created: 20220223 Date Completed: 20220224 Latest Revision: 20220301
    • Publication Date:
      20221216
    • Accession Number:
      PMC8864876
    • Accession Number:
      10.1186/s12864-022-08375-1
    • Accession Number:
      35193521