conda create -n SNP #创建一个叫SNP的环境 conda activate SNP #激活SNP这个环境,在这个环境内安装软件 conda install -c biocondabcftoolsplink2phylipiqtreetasselvcftools 在安装完成之后,如果运行bcftools出现报错,提示没有这个“libgsl.so.25”的数据库时候,需要自己进行安装相关依赖的数据库才能使用bcftools软件。
wget https://github.com/IEkAdN/BactSNP/releases/download/v1.1.0/bactsnp-1.1.0.linux64.tgz tar xf bactsnp-1.1.0.linux64.tgzcdbactsnp-1.1.0.linux64 make# 将bactsnp可执行程序复制到 */Anaconda3/envs/BactSNP/bin/中conda_bin=`which samtools`cp bactsnp${conda_bin%/*} 3. 测试 wget -...
$ conda install psdm Precompiled binaries tl;dr: Run the following snippet to download the latest binary for your system to the current directory and show the help menu. version="0.3.0"OS=$(uname -s)if["$OS"="Linux"];thentriple="x86_64-unknown-linux-musl"elif["$OS"="Darwin"];then...
conda install -c bioconda pairsnp The c++ code relies on a recent version of Armadillo (currently tested on v8.6) and after downloading the repository can be built by runningcd ./pairsnp-cpp/ ./configure make make install The majority of time is spend doing sparse matrix multiplications so ...
conda install-c bioconda plink 1. 建立索引 cpGenome.fa 即叶绿体基因组 bwa index cpGenome.fa 2. 将双端测序数据,比对到 叶绿体基因组 nohup bwa mem-t4-M cpGenome.fa CRRXXX_f1.fastq.gz CRRXXX_r2.fastq.gz2>CRRXXX_map.log|samtools sort-O bam-@4-o CRRXXX.sorted.bam1>CRRXXX.sort.log2>...
conda install bcftools 注意,后两者安装后,建议直接再 Update 一下 conda update samtools conda update bcftools 下载并准备 Picard 软件,用于标记重复,事实上,似乎可以直接使用 sambamba 软件 wget https://github.com/broadinstitute/picard/releases/download/2.25.7/picard.jar ...
condainstall bwacondainstall samtoolscondainstall bcftools 注意,后两者安装后,建议直接再 Update 一下 condaupdate samtoolscondaupdate bcftools 下载并准备 Picard 软件,用于标记重复,事实上,似乎可以直接使用 sambamba 软件 wgethttps://github.com/broadinstitute/picard/releases/download/2.25.7/picard.jar ...
(https://www.python.org/downloads/) Alternatively python can be installed using a package manager such as miniconda (https://conda.io/miniconda.html). sudo apt install python sudo apt install python-setuptools sudo apt install python-dev A recent version of Java is needed sudo add-apt-...
然后下载相关的分析软件，使用conda安装 conda create -n SNP #创建一个叫SNP的环境 conda activate SNP...
conda install -c bioconda mummer mummer -help nucmer -help 1 比对: nucmer -p [out_index] [ref] [query] nucmer -p align ref.fna input.fna -p|prefix:Set the prefix of the output files (default "out") --mum: Use anchor matches that are unique in both the reference and query ...