一、组装 本次组装主要使用 hifiasm,一款专门用于拼接 pacbio hifi 数据的软件 软件链接:https://github.com/chhylp123/hifiasm 组装脚本: #!/bin/bash #PBS -l nodes=1:ppn=30 #PBS -l walltime=999:00:00 cd /data/0.user_data/lx_sky6/weipei/genomics/1128-hupinan/1.assembly_hifiasm export P...
A new preprint evaluates the utility of PacBio HiFi reads for assembly of a human genome. The team generated 24-fold coverage of CHM13 with the Sequel II System, producing an average of 19.1 Gb of HiFi reads with each SMRT Cell 8M.
[1]Wenger A M , Peluso P , Rowell W J , et al. Accurate circular consensus long-read sequencing improves variant detection and assembly of a human genome[J]. Nature Biotechnology, 2019, 37(11). [2]PacBio.In precisionFDA Challenge,PacBio HiFi Reads Outperform Both Short Reads and Noisy ...
Truly complete assembly of complex genomes Accurately construct the full sequence of chromosomes, including telomeres and centromeres. Targeted sequencing to study genes at scale Focus the power of HiFi variant calling by enriching for regions of interest using hybrid capture or PCR amplification. Si...
hifiasm是一个能有效利用PacBio HiFi测序技术,在分型组装图(pahsed assembly gprah)中可靠的表示单倍体信息的算法。 流程介绍 hifiasm的分析流程如下,主要分为3个阶段 第一阶段:通过所有序列的相互比对,对前在测序错误进行纠正。如果一个位置只存在两种碱基类型,且每个碱基类型至少有3条read支持,那么这个位置会被当...
然而,高组装质量基因组的获得,通常需要以高深度测序为代价。而PacBio高准确度的HiFi reads及相关的组装方法,大大降低了实现高质量从头组装的成本,进而有利于未来的De novo assembly研究。 此外,泛基因组构建要点还包含①数据不要受到技术偏好性左右,以减少系统性的误差;②要采用高质量数据和组装方法,准确地反映样本个...
##assembly 用velvet,可以从fastq开始 也可以从bam开始 ##fastq文件作为input #velveth ${PBS_O_WORKDIR}${samplename} 31 -shortPaired -fastq -separate ${doc}/${samplename}.ngs.1.fastq ${doc}/${samplename}.ngs.2.fastq ##bam文件作为input,注意修改输入文件路径呀,这里一般一个样本件一个文件夹...
minimap2_options_map = -t 10 # minimap2 options, used to map reads back to the assembly. nextgraph_options = -a 1 #nextgraph options, see nextgraph for details. 一个实例run.cfg文件: job_type = local # here we use SGE to manage jobs job_prefix = nextDenovo task = all rewrite ...
1. "Hybrid error correction and de novo assembly of single-molecule sequencing reads"(Nature Biotechnology,2012) 该论文首次提出了一个基于overlap-layout-consensus(OLC)模型的长read纠错方法,并将其应用于de novo基因组组装中。该方法的核心思想是通过多个覆盖度较高的长read重叠区域,来构建出更为准确的序列。
et al. Accurate circular consensus long-read sequencing improves variant detection and assembly of...