|
01
软件网站链接
http://busco.ezlab.org
02
软件所需其它环境
Augustus (> 3.2.1) HMMER (HMMER v3.1b2) NCBI BLAST+
export PATH="/path/to/AUGUSTUS/augustus-3.2.3/bin:$PATH"
export PATH="/path/to/AUGUSTUS/augustus-3.2.3/s:$PATH"
export AUGUSTUS_CONFIG_PATH="/path/to/AUGUSTUS/augustus-3.2.3/config/"
03
所需数据库下载链接
# Bacteria
wget http://busco.ezlab.org/v2/datasets/bacteria_odb9.tar.gz
wget http://busco.ezlab.org/v2/datasets/proteobacteria_odb9.tar.gz
wget http://busco.ezlab.org/v2/datasets/rhizobiales_odb9.tar.gz
wget http://busco.ezlab.org/v2/datasets/betaproteobacteria_odb9.tar.gz
wget http://busco.ezlab.org/v2/datasets/gammaproteobacteria_odb9.tar.gz
wget http://busco.ezlab.org/v2/datasets/enterobacteriales_odb9.tar.gz
wget http://busco.ezlab.org/v2/datasets/deltaepsilonsub_odb9.tar.gz
wget http://busco.ezlab.org/v2/datasets/actinobacteria_odb9.tar.gz
wget http://busco.ezlab.org/v2/datasets/cyanobacteria_odb9.tar.gz
wget http://busco.ezlab.org/v2/datasets/firmicutes_odb9.tar.gz
wget http://busco.ezlab.org/v2/datasets/clostridia_odb9.tar.gz
wget http://busco.ezlab.org/v2/datasets/lactobacillales_odb9.tar.gz
wget http://busco.ezlab.org/v2/datasets/bacillales_odb9.tar.gz
wget http://busco.ezlab.org/v2/datasets/bacteroidetes_odb9.tar.gz
wget http://busco.ezlab.org/v2/datasets/spirochaetes_odb9.tar.gz
wget http://busco.ezlab.org/v2/datasets/tenericutes_odb9.tar.gz
# Eukaryota
wget http://busco.ezlab.org/v2/datasets/eukaryota_odb9.tar.gz
wget http://busco.ezlab.org/v2/datasets/fungi_odb9.tar.gz
wget http://busco.ezlab.org/v2/datasets/microsporidia_odb9.tar.gz
wget http://busco.ezlab.org/v2/datasets/dikarya_odb9.tar.gz
wget http://busco.ezlab.org/v2/datasets/ascomycota_odb9.tar.gz
wget http://busco.ezlab.org/v2/datasets/pezizomycotina_odb9.tar.gz
wget http://busco.ezlab.org/v2/datasets/eurotiomycetes_odb9.tar.gz
wget http://busco.ezlab.org/v2/datasets/sordariomyceta_odb9.tar.gz
wget http://busco.ezlab.org/v2/datasets/saccharomyceta_odb9.tar.gz
wget http://busco.ezlab.org/v2/datasets/saccharomycetales_odb9.tar.gz
wget http://busco.ezlab.org/v2/datasets/basidiomycota_odb9.tar.gz
wget http://busco.ezlab.org/v2/datasets/metazoa_odb9.tar.gz
wget http://busco.ezlab.org/v2/datasets/nematoda_odb9.tar.gz
wget http://busco.ezlab.org/v2/datasets/arthropoda_odb9.tar.gz
wget http://busco.ezlab.org/v2/datasets/insecta_odb9.tar.gz
wget http://busco.ezlab.org/v2/datasets/endopterygota_odb9.tar.gz
wget http://busco.ezlab.org/v2/datasets/hymenoptera_odb9.tar.gz
wget http://busco.ezlab.org/v2/datasets/diptera_odb9.tar.gz
wget http://busco.ezlab.org/v2/datasets/vertebrata_odb9.tar.gz
wget http://busco.ezlab.org/v2/datasets/actinopterygii_odb9.tar.gz
wget http://busco.ezlab.org/v2/datasets/tetrapoda_odb9.tar.gz
wget http://busco.ezlab.org/v2/datasets/aves_odb9.tar.gz
wget http://busco.ezlab.org/v2/datasets/mammalia_odb9.tar.gz
wget http://busco.ezlab.org/v2/datasets/euarchontoglires_odb9.tar.gz
wget http://busco.ezlab.org/v2/datasets/laurasiatheria_odb9.tar.gz
wget http://busco.ezlab.org/v2/datasets/embryophyta_odb9.tar.gz
wget http://busco.ezlab.org/v2/datasets/protists_ensembl.tar.gz
wget http://busco.ezlab.org/v2/datasets/alveolata_stramenophiles_ensembl.tar.gz
04
数据库对应物种关系
05
解压其中一个数据
tarzvxf vertebrata_odb9.tar.gz
06
python run_BUSCO.py -iYOUR_SEQUENCE_FILE.fa -o OUTPUT_NAMe -l /NAME_OF_LINEAGE -m geno
-m or --mode sets the assessment MODE: genome(geno), proteins(prot), tranome(tran)
07
关于软件运行时间的问题
Example assessment runtimes (gene sets with 5 CPUs, genomes with 12 CPUs):
| 
收藏