Journal of Hebei University(Natural Science Edition) >

2023 , Vol. 43 >Issue 2: 171 - 178

DOI: https://doi.org/10.3969/j.issn.1000-1565.2023.02.009

Comparison of application of assemblers in phylogenomics

  • WANG Yaozhuo ,
  • ZHANG Wenqiang ,
  • ZHANG Junxia
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  • Key Laboratory of Zoological Systematics and Application of Hebei Province, Institute of Life Science and Green Development, College of Life Sciences, Hebei University, Baoding 071002, China

Received date: 2022-05-17

  Online published: 2023-04-06

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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

Cite this article

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 . DOI: 10.3969/j.issn.1000-1565.2023.02.009

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