CD-hit安装及使用

cd-hit下载：

网址：https://github.com/weizhongli/cdhit/releases

# 下载ch-hit
wget https://github.com/weizhongli/cdhit/releases/download/V4.8.1/cd-hit-v4.8.1-2019-0228.tar.gz

# 解压
tar -zxvf cd-hit-v4.8.1-2019-0228.tar.gz

# 编译
cd cd-hit-auxtools
make

基本用法

cd-hit -i nr -o nr100 -c 1.00 -n 5 -M 16000 –d 0 -T 8
cd-hit -i db -o db90 -c 0.9 -n 5 -M 16000 –d 0 -T 8
where
db is the filename of input,
db90 is output, 
-c 1.0, means 100% identity, is the clustering threshold
-c 0.9, means 90% identity, is the clustering threshold
-n 5 is the word size
-d 0 use sequence name in fasta header till the first white space
-M 16000, to use 16GB RAM
-T 8, to use 8 threads

Choose of word size:
-n 5 for thresholds 0.7 ~ 1.0
-n 4 for thresholds 0.6 ~ 0.7
-n 3 for thresholds 0.5 ~ 0.6
-n 2 for thresholds 0.4 ~ 0.5

需查看更多选项：

cd-hit -h