LiBis：用于低输入BS-seq的超灵敏比对方法

文章发表题目：LiBis: An ultrasensitive alignment method for low input bisulfite sequencing
Github地址：https://github.com/Dangertrip/LiBis
文章地址：https://academic.oup.com/bib/advance-article/doi/10.1093/bib/bbaa332/6034045
孙德强教授课题组贡献的软件，孙教授发表过不少的BS-seq相关的工具。
libis的优点是可以显著提高低输入DNA亚硫酸氢盐测序定位读数比率的方法

安装
libis依赖于python3.6+

使用conda安装（推荐）

conda config --add channels defaults
conda config --add channels bioconda
conda config --add channels conda-forge
conda install libis

依赖软件：LiBis integrates FastQC, Bedtools, Trim-galore, moabs and samtools. These packages can be installed independently or by conda.
```

conda install -c bioconda fastqc
conda install -c bioconda bedtools
conda install -c bioconda cutadapt
conda install -c bioconda trim-galore
conda install -c bioconda moabs
conda install -c bioconda samtools=1.1

使用 Docker 安装
LiBis also supports the Docker installation.
```

wget https://github.com/Dangertrip/LiBis/archive/master.zip
unzip master.zip
cd LiBis-master/
docker build --tag=libis ./
docker run libis LiBis --help

跑一下测试数据集

git clone https://github.com/Dangertrip/LiBis.git
cd LiBis/Example/
# Run LiBis from begining:
LiBis -n sample1_mate1.fq.gz,sample1_mate2.fq.gz sample2_mate1.fq.gz,sample2_mate2.fq.gz -r /PATH_TO_FASTA_REFERENCE

随便记录一下软件作者在BS-seq相关的小脚本：https://github.com/Dangertrip/Bioinformatics_scripts