An exploration of assembly strategies and quality metrics on the accuracy of the rewarewa (Knightia excelsa) genome.

ABSTRACT: We used long read sequencing data generated from Knightia excelsa, a nectar-producing Proteaceae tree endemic to Aotearoa (New Zealand), to explore how sequencing data type, volume and workflows can impact final assembly accuracy and chromosome reconstruction. Establishing a high-quality genome for this species has specific cultural importance to Māori and commercial importance to honey producers in Aotearoa. Assemblies were produced by five long read assemblers using data subsampled based on read lengths, two polishing strategies and two Hi-C mapping methods. Our results from subsampling the data by read length showed that each assembler tested performed differently depending on the coverage and the read length of the data. Subsampling highlighted that input data with longer read lengths

SUBMITTER: McCartney AM 

PROVIDER: S-EPMC8362059 | biostudies-literature | 2021 Aug

REPOSITORIES: biostudies-literature