69方法
标题：Comprehensive evaluation of structural variation detection algorithms for whole genome sequencing
译文：全基因组测序SV检测方法评估
期刊：Genome biology 2019
sgvfinder2
标题：Structural variation in the gut microbiome associates with host health
译文：肠道菌群SV与宿主健康相关
期刊：Nature 2019
github: https://github.com/korem-lab/SGVFinder2
安装
# 环境
source /hwfsxx1/ST_HN/P18Z10200N0423/huty/software/miniconda3_2/etc/profile.d/conda.sh
conda activate sgvfinder2
conda install gcc=11 -c conda-forge # OK
conda install libgcc gxx_linux-64 -c conda-forge # OK
conda install python=3.10.12 # OK
conda install pandas=2.1.0 # 包含numpy
conda install Cython=3.0.2 ujson=5.8.0 pysam=0.21.0 # OK
conda install bowtie2 # 指定2.2.5会报错，默认下载2.5.3
conda install scipy=1.11.2 -c biconda # OK
conda install bokeh=3.2.2 -c bioconda # OK
#conda install Bio=1.5.9 # False
conda install biopython # python3 import Bio测试成功
pip install --no-cache-dir git+https://github.com/korem-lab/SGVFinder2.git
# 一次不行即，2次成功
export PATH="/hwfsxx1/ST_HN/P18Z10200N0423/huty/software/miniconda3_2/envs/sgvfinder2/bin":$PATH
svfinder -h
icra -h
# AssertionError: Cannot find `samtools` installation
conda install samtools
测试
svfinder -h
svfinder get_sample_map -h
svfinder work_on_collection -h
icra -h
icra single_file -h
