GetOrganelle安装
conda install -c bioconda getorganelle
or download from github
unzip GetOrganelle-master.zip;cd GetOrganelle-masterpython setup.py installget_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 /Kinggerm/GetOrganelleGallery/raw/master/Test/reads/Arabidopsis_simulated.1.fq.gzwget /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!
GeSeq网站注释
https://chlorobox.mpimp-golm.mpg.de/geseq.html