构建Pan-genome的方法主要有3种:Iterative、map-to-pan和De novoassembly,Iterative和map-to-pan的方法是通过将短的reads比对到已经注释的基因组上进而鉴定基因的PAVs。然而这种方法对于多拷贝基因的检测是有局限的,且由于作物基因组的高度重复性和SVs的普遍存在,极易出错 (Gan et al., 2011;Zapata et al., 201...
4.3.9. Genome assembly 装配前使用Jellyfish v2.2.6计算k-mer频率(k = 17)。然后,利用NGS数据,利用genomeScope v1.0软件对基因组大小、重复度、杂合度等性状进行预测。 用以下管道进行从头基因组组装:(a)用Canu v1.8校正ONT reads。(b)使用Smartdenovo v1.0将校正后的ONT reads集中到contigs,参数如下:wtpre...
seqkit grep-r-f chr.list../../An-1.chr.all.v2.0.fasta-o00.assembly/An1.fa seqkit grep-r-f chr.list../../C24.chr.all.v2.0.fasta-o00.assembly/C24.fa seqkit grep-r-f chr.list../../Cvi.chr.all.v2.0.fasta-o00.assembly/Cvi.fa seqkit grep-r-f chr.list../../Eri.chr.al...
构建Pan-genome的方法主要有3种:Iterative、map-to-pan和De novoassembly,Iterative和map-to-pan的方法是通过将短的reads比对到已经注释的基因组上进而鉴定基因的PAVs。然而这种方法对于多拷贝基因的检测是有局限的,且由于作物基因组的高度重复性和SVs的普遍存在,极易出错 (Gan et al., 2011;Zapata et al., 201...
Here, we employed a reference゛ssisted assembly approach to improve the draft assemblies of four of the sesame varieties. We then constructed a sesame panゞenome of 554.05 Mb. The panゞenome contained 26,472 orthologous gene clusters; 15,409 (58.21%) of them were core (present across all...
The 13 apple accessions used for pan-genome assembly include four wild apple species and nine apple cultivars (M. domestica). The four wild species are M. sylvestris (MSM), M. sieversii (MSR), M. orientalis (MO), and M. asiatica“Zisai Pearl” (MA). The nine c...
Assembly of diverse Chinese genomes 68个样本:代表了36个少数民族和8个具有语言群体的中国泛基因组联盟核心样本 hifi:28.82X(14.29–60.67×) 9个sample 测了 linked reads; 11个sample测了ONT三代以及hic数据 组装了58个单倍型水平的组装体(图 1a)
A chromosome-level genome assembly of 14 February 2025 Introduction Genomic data greatly accelerated the development of biological research in the last two decades. Recently, the focus of genome research has shifted from a single reference genome to a pan-genome approach that provides greater insights...
构建pan-genome的方法主要有三种：Iterative、map-to-pan和De novo assembly。Iterative和map-to-pan方法适用于相对低的测序深度下实现pan-genome的研究，而De novo assembly可以提供更准确的pan-genome信息。随着测序技术的发展，特别是长读测序技术和组装方法，实现高质量从头组装的成本降低，有利于未来的De...
Genome assembly Contig genome assembly of the ten accessions was performed from CCS clean reads using the hifiasm92software with parameters settings: “-l 2 --purge-cov 100 --high-het -s 0.01”. For GS and FJ de novo genome assembly was performed to anchor contigs into chromosomes using Hi...