wtdbg2.pl \-i pacbio.fastq.gz \-t12\-x rs \-g5.4m \-o pacbio_wtdbg2/pacbio_wtdbg2 wtdbg2主要输出结果文件 代码语言:javascript 复制 #最终组装结果文件,用于下游分析 pacbio_wtdbg2.cns.fa
在2天内,wtdbg2算法可以 1.2TB 内存组装32Gb 的蝾螈基因组,NG50为392kb,大于已发布的序列长度。 据悉,该研究开始于2013年,自2016年起,wtdbg2可免费开放使用https://github.com/ruanjue/wtdbg2。wtdbg已被数十篇论文引用,并被多家基因测序公司使用。2019年 1月26日,该研究首先发表在了 bioRxiv 上。 十年前...
WTDBG: De novo assembler for long noisy sequences Author: Jue Ruan <ruanjue@gmail.com> Version: 2.5 (20190621) Usage: wtdbg2 [options] -i <reads.fa> -o <prefix> [reads.fa ...] Options: -i <string> Long reads sequences file (REQUIRED; can be multiple), [] -o <string> Prefix...
Wtdbg2是一个三代测序数据(同时适用于pacbio和nanopore)denovo组装软件,它是一款基于C语言开发的开源软件。相较于其他三代数据组装软件(Canu,smartdenovo,miniasm,FALCON,FALCON-unzip),优点如下: 安装简单(反例FALCON,安装过程非常复杂) 使用简单,可用“run_wtdbg_assembly.sh”脚本生成运行脚本 ...
wtdbg2优点是速度非常快,安装使用都非常简单。 用于nanopore及pacbio数据的组装 原理 首先要注意,wtdbg2不同于megahit等二代组装软件DBG的原理,wtdbg2得到的图称为fuzzy-Bruijn graph (FBG), 作者在文中提到: A‘base’ in FBG is a 256 bp bin(each small box ) and a ‘K-mer’ or K-bin in FBG ...
1#安装wtdbg2 ## 手动安装 git clone https://github.com/ruanjue/wtdbg2 cd wtdbg2 && make ## 自动安装 conda install -c bioconda wtdbg 2#用wtdbg2进行初步组装 分两步,第一步是组装,第二步是得到一致性序列。 ## wtdbg2组装 /newlustre/home/jfgui/wy/anaconda3/envs/pengfang/bin/wtdbg2 \ ...
Existing long-read assemblers require thousands of central processing unit hours to assemble a human genome and are being outpaced by sequencing technologies in terms of both throughput and cost. We developed a long-read assembler wtdbg2 (https://github.
wtdbg.h wtdbg2.pl wtpoa-cns.c wtpoa.h Breadcrumbs wtdbg2 / Latest commit lh3 Updated README Sep 24, 2018 2e795f1·Sep 24, 2018 History History NEWS |2018-09-21| Rename wtdbg-1.2.8 to wtdbg2 |2018-09-19| GFA supports wtdbg-dot2gfa.pl dbg.3.dot>dbg.3.gfa ...
git clone https://github.com/ruanjue/wtdbg2 cd wtdbg2 && make #quick start with wtdbg2.pl ./wtdbg2.pl -t 16 -x rs -g 4.6m -o dbg reads.fa.gz # Step by step commandlines # assemble long reads ./wtdbg2 -x rs -g 4.6m -i reads.fa.gz -t 16 -fo dbg # derive consensus ...
wtdbg2Performance optimizationComputational biologyAuto-tuningLoad balanceDe novo genome assembly reconstructs the chromosomes from massive relatively short fragmented reads and serves as fundamental for studying new species where there is no reference genome. Wtdbg2 is a ......