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

BMC Genomics

Sheina B. Sim¹  Renee L. Corpuz¹  Scott M. Geib¹  Tyler J. Simmonds² 

[1] USDA-ARS Daniel K. Inouye US Pacific Basin Agricultural Research Center, 64 Nowelo Street, 96720, Hilo, HI, USA;USDA-ARS Daniel K. Inouye US Pacific Basin Agricultural Research Center, 64 Nowelo Street, 96720, Hilo, HI, USA;Oak Ridge Institute for Science and Education, Oak Ridge Associated Universities, 37830, Oak Ridge, TN, USA;

关键词: PacBio HiFi;    Circular consensus sequencing;    Adapter;    Sequence data filtering;   

DOI  :  10.1186/s12864-022-08375-1

来源: Springer

【 摘 要 】

BackgroundPacific 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.ResultsAnalysis 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.ConclusionsHere 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.

【 授权许可】

CC BY