cd hit使用

~~和唐老师一个实验室的人开发的~~

CD-HIT is a very widely used program for clustering and comparing protein or nucleotide sequences. CD-HIT was originally developed by Dr. Weizhong Liat Dr. Adam Godzik's Lab at the Burnham Institute (now Sanford-Burnham Medical Research Institute)

CD-HIT is very fast and can handle extremely large databases. CD-HIT helps to significantly reduce the computational and manual efforts in many sequence analysis tasks and aids in understanding the data structure and correct the bias within a dataset.

The CD-HIT package has CD-HIT, CD-HIT-2D, CD-HIT-EST, CD-HIT-EST-2D, CD-HIT-454, CD-HIT-PARA, PSI-CD-HIT, CD-HIT-OTU, CD-HIT-LAP, CD-HIT-DUP and over a dozen scripts.

• CD-HIT (CD-HIT-EST) clusters similar proteins (DNAs) into clusters that meet a user-defined similarity threshold.
• CD-HIT-2D (CD-HIT-EST-2D) compares 2 datasets and identifies the sequences in db2 that are similar to db1 above a threshold.
• CD-HIT-454 identifies natural and artificial duplicates from pyrosequencing reads.
• CD-HIT-OTU clusters rRNA tags into OTUs
• CD-HIT-DUP identifies duplicates from single or paired Illumina reads
• CD-HIT-LAP identifies overlapping reads

The usage of other programs and scripts can be found in CD-HIT user's guide.

CD-HIT is currently maintained by the Dr. Li's group (http://weizhongli-lab.org/) at J Craig Venter Institute. We thank the support from National Center for Research Resources (Grant # 1R01RR025030, 2008-2011). We thank all users that report bugs, give us suggestions and comments.

下载：

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

解压

安装： sudo make

具体使用：

如果是蛋白质序列，就用cd-hit

我的是核算序列，用cd-hit-est

cd-hit-est -i 输入文件 -o 输出文件 -c 相似度（0.99） -T 0（用全部的线程去跑）

freemao

FAFU