【6】零散记录-EDTA-BUSCO-RepeatMasker_edta和repeatmasker

1. EDTA安装

git clone https://github.com/oushujun/EDTA.git
cd EDTA
conda env create -f EDTA.yml

2. EDTA 使用

conda activate EDTA
perl ~/miniconda3/envs/EDTA/bin/EDTA_raw.pl -genome rice_genome.fasta -species Rice -threads 6

3. RepeatMasker安装

conda install TRF
conda install RMBlast
 
wget http://www.repeatmasker.org/RepeatMasker-open-4-0-6.tar.gz
tar xzvf RepeatMasker-open-4-0-6.tar.gz
cd RepeatMasker
chmod -R 755 *
./configure

4. BUSCO安装

conda create -n busco  python=3.8
conda activate busco
conda install -c bioconda -c conda-forge busco=4.1.2 augustus=3.3.3

5. BUSCO使用

##激活环境
conda install busco
##运行busco
busco -i ./015Actinidia-macrosperma_RNA--/trinity_out_dir/Trinity.fasta -l /home/xiaolong/database/BUSCO/embryophyta_odb10 --out_path ./015Actinidia-macrosperma_RNA--/trinity_out_dir/ -o busco -m tran --cpu 80