GetOrganelle软件从ngs数据中组装线粒体、叶绿体基因组；GeSeq网站注释细胞系基因组

little^raccoon

8075人浏览 · 2020-08-29 16:08:07

little^raccoon · 2020-08-29 16:08:07 发布

GetOrganelle安装

conda install -c bioconda getorganelle

or download from github

 unzip GetOrganelle-master.zip;
 cd GetOrganelle-master
 python setup.py install
 get_organelle_config.py --add embplant_pt,embplant_mt  #v1.7.0版本后，默认的database需要手动下载，我在这里这下载了植物pt和mt的
 Utilities/get_organelle_config.py -a embplant_pt,embplant_mt

官方测试

下载数据

wget https://github.com/Kinggerm/GetOrganelleGallery/raw/master/Test/reads/Arabidopsis_simulated.1.fq.gz
wget https://github.com/Kinggerm/GetOrganelleGallery/raw/master/Test/reads/Arabidopsis_simulated.2.fq.gz

运行

get_organelle_from_reads.py -1 Arabidopsis_simulated.1.fq.gz -2 Arabidopsis_simulated.2.fq.gz -t 1 -o Arabidopsis_simulated.plastome -F embplant_pt -R 10

我用单核 3.2G内存跑的
Total cost 18665.70 s
Thank you!