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用busco评估基因组组装完整性攻略

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浏览:- 发布日期:2017-12-27 15:36:06【 】

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):


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