Comparison of application of assemblers in phylogenomics

doi:10.3969/j.issn.1000-1565.2023.02.009

Abstract

Abstract: To select the most suitable assembler for ultra-conserved elements(UCE)phylogenomic practice, five different assembly softwares, SPAdes, ABySS, Velvet, Trinity and Minia were applied, to assemble 17 UCE captured sequencing libraries, respectively. The results showed that among the five assemblers, Trinity consumed significantly longer computational time than the others; SPAdes and Trinity both assembled more contigs and obtained more longer contigs(> 250 bp)than the other three assemblers, but SPAdes captured the highest number of UCE loci. Therefore, SPAdes is more suitable for the assembly of UCE data than the other assembly softwares. This study provides a technical reference for the practice of UCE-based phylogenomic studies.

Key words: data analysis, UCE, phylogenomics

CLC Number:

Q951

WANG Yaozhuo, ZHANG Wenqiang, ZHANG Junxia. Comparison of application of assemblers in phylogenomics[J]. Journal of Hebei University(Natural Science Edition), 2023, 43(2): 171-178.

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