## CVG for BUSCO
## Authorized by Yuichiro Hara & Shigehiro Kuraku
 
1. Installation
   a) Install BUSCO
   Download the installation package at BUSCO home page https://busco.ezlab.org/.
   Install BUSCO and a few bioinformatics packages accoding to the guidance of BUSCO manual.

   b) Download and unpack the downloaded file of the CVG suite.
   $ wget  https://transcriptome.riken.jp/reptiliomix/resources/CVG_11112022.tar.gz
   $ tar zxf CVG_11112022.tar.gz
 
   c) Copy the CVG data directory
   for BUSCO v1-v4
   $ cd CVG_11112022/busco
   $ cp -r other /TO/SOMEWHERE/

   for BUSCO v5
   $ cd CVG_11112022/busco
   $ cp -r other_odb10 /TO/SOMEWHERE/
  
 
2. Usage

   BUSCO v1
   $ python3 BUSCO_v1.22.py -o SAMPLE -in genome.fa -l /TO/SOMEWHERE/other -m genome

   BUSCO v2-v4
   $ python3 BUSCO.py -o SAMPLE -i genome.fa -l /TO/SOMEWHERE/other -m geno

   BUSCO v5
   $ busco --offline -o SAMPLE -i genome.fa -l /TO/SOMEWHERE/other -m geno

 
3. Copyrights
 
The CVG, the new reference gene set for vertebrates, and modified cegma scripts were prepared by Yuichiro Hara (yuichiro.hara@riken.jp) and Shigehiro Kuraku (shigehiro.kuraku@riken.jp) in Phyloinformatics Unit, RIKEN CLST. More information on this project is found at http://www.clst.riken.jp/phylo/reptiliomix.html
 

4. Citation
   Please cite the articles below when you present or publish any data based on the use of BUSCO referring to the CVG.
  
   - BUSCO
   Simao, Felipe A., et al. "BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs." Bioinformatics (2015): btv351.
 
   - Extended completeness analysis with this package and use of CVGs
   Yuichiro Hara, Kaori Tatsumi, Michio Yoshida, Eriko Kajikawa, Hiroshi Kiyonari, and Shigehiro Kuraku. "Optimizing and benchmarking de novo transcriptome sequencing: from library preparation to assembly evaluation." under review.

