Additional file 4: of An internet-based bioinformatics toolkit for plant biosecurity diagnosis and surveillance of viruses and viroids

Paired sample t-test of contigs produced by SPAdes, Velvet, ABySS and SOAPdenovo assemblers. Our optimised ‘SPAdes K15-17-19_cap3’ (SPAdes assembly; dataset = 21–22 nt; kmer set =15,17 and 19; and scaffolded with CAP3) (SP22_K15-17-19_cap3) assembly was compared against all other kmer settings and/or tools. A) SPAdes - Longest assembled contigs (21–22 nt pipeline); B) SPAdes - Total number of assembled bases for contigs > =100 nt (21–22 nt pipeline); C) SPAdes - Longest assembled contigs (21–25 nt pipeline); D) SPAdes - Total number of assembled bases for contigs > =100 nt (21–25 nt pipeline); E) Comparison of longest assembled contig using Velvet against SP22_K15-17-19_cap3; F) Comparison of longest assembled contig using ABySS against SP22_K15-17-19_cap3; G) Comparison of longest assembled contig using SOAPdenovo against SP22_K15-17-19_cap3. (XLSX 19 kb)

针对SPAdes、Velvet、ABySS与SOAPdenovo四款基因组组装工具生成的重叠群（contigs）开展配对样本t检验。本研究优化得到的‘SPAdes K15-17-19_cap3’组装方案（SPAdes组装；数据集为21–22 nt；kmer集合为15、17、19；并通过CAP3进行支架组装），记为SP22_K15-17-19_cap3，将该组装结果与其余所有kmer设置及/或其他组装工具的结果进行对比。A) SPAdes——（21–22 nt分析流程）最长组装重叠群；B) SPAdes——（21–22 nt分析流程）长度≥100 nt的重叠群总组装碱基数；C) SPAdes——（21–25 nt分析流程）最长组装重叠群；D) SPAdes——（21–25 nt分析流程）长度≥100 nt的重叠群总组装碱基数；E) 采用Velvet组装得到的最长重叠群与SP22_K15-17-19_cap3的对比；F) 采用ABySS组装得到的最长重叠群与SP22_K15-17-19_cap3的对比；G) 采用SOAPdenovo组装得到的最长重叠群与SP22_K15-17-19_cap3的对比。（XLSX 19 kb）