使用busco进行基因组质量评估

BUSCO是一款使用python语言编写的对转录组和基因组组装质量进行评估的软件。在相近的物种之间总有一些保守的序列，而BUSCO就是使用这些保守序列与组装的结果进行比对，鉴定组装的结果是否包含这些序列，包含单条、多条还是部分或者不包含等等情况来给出结果。

软件所需软件及环境：

• python
• blast
• metaeuk
• augustus
• sepp
• hmmer
• Rscript
  所使用软件均可通过conda安装。

#运行脚本
 busco --config ~/Applications/busco/config/config.ini -i genome.fna -o 1 -m genome

busco --config ~/Applications/busco/config/config.ini -i Oryza_sativa.IRGSP-1.0.pep.all.fa -o H1 -m protein -l /home/ubuntu/peo/busco_downloads/lineages/eukaryota_odb10/

--config 文件配置是指将所需软件位置指定在config.ini文件夹下，软件会识别该文件所指定软件目录，具体配置如下：

# This is the BUSCOv5 configuration file template.
# It is not necessary to use this, as BUSCO will use the dependencies available on your PATH by default.
# The busco run parameters can all be set on the command line. See the help prompt (busco -h) for details.
#
# To use this file for an alternative configuration, or to specify particular versions of dependencies:
# 1) edit the path and command values to match your desired dependency versions.
#    WARNING: passing a parameter through the command line overrides the value specified in this file.
#
# 2) Enable a parameter by removing ";"
#
# 3) Make this config file available to BUSCO either by setting an environment variable
#
#                   export BUSCO_CONFIG_FILE="/path/to/myconfig.ini"
#
#    or by passing it as a command line argument
#
#                   busco  --config /path/to/config.ini
#
[busco_run]
# Input file
;in = /path/to/input_file.fna
# Run name, used in output files and folder
;out = BUSCO_run
# Where to store the output directory
;out_path = /path/to/output_folder
# Path to the BUSCO dataset
;lineage_dataset = bacteria
# Which mode to run (genome / proteins / transcriptome)
;mode = genome
# Run lineage auto selector
;auto-lineage = True
# Run auto selector only for non-eukaryote datasets
;auto-lineage-prok = True
# Run auto selector only for eukaryote datasets
;auto-lineage-euk = True
# How many threads to use for multithreaded steps
;cpu = 16
# Force rewrite if files already exist (True/False)
;force = False
# Restart a previous BUSCO run (True/False)
;restart = False
# Blast e-value
;evalue = 1e-3
# How many candidate regions (contigs, scaffolds) to consider for each BUSCO
;limit = 3
# Metaeuk parameters for initial run
;metaeuk_parameters='--param1=value1,--param2=value2'
# Metaeuk parameters for rerun
;metaeuk_rerun_parameters=""
# Augustus parameters
;augustus_parameters='--param1=value1,--param2=value2'
# Quiet mode (True/False)
;quiet = False
# Local destination path for downloaded lineage datasets
;download_path = ./busco_downloads/
# Run offline
;offline=True
# Ortho DB Datasets version
;datasets_version = odb10
# URL to BUSCO datasets
;download_base_url = https://busco-data.ezlab.org/v4/data/
# Download most recent BUSCO data and files
;update-data = True
# Use Augustus gene predictor instead of metaeuk
;use_augustus = True

[tblastn]
path = /home/ubuntu/miniconda3/envs/python36/bin
command = tblastn

[makeblastdb]
path = /home/ubuntu/miniconda3/envs/python36/bin
command = makeblastdb


[augustus]
path = /home/ubuntu/miniconda3/envs/python36/bin
command = augustus

[etraining]
path = /home/ubuntu/miniconda3/envs/python36/bin
command = etraining

[gff2gbSmallDNA.pl]
path = /home/ubuntu/miniconda3/envs/python36/bin
command = gff2gbSmallDNA.pl

[new_species.pl]
path = /home/ubuntu/miniconda3/envs/python36/bin
command = new_species.pl

[optimize_augustus.pl]
path = /home/ubuntu/miniconda3/envs/python36/bin
command = optimize_augustus.pl

[hmmsearch]
path = /home/ubuntu/miniconda3/envs/python36/bin
command = hmmsearch

[prodigal]
path = /home/ubuntu/miniconda3/envs/python36/bin
command = prodigal

[metaeuk]
path = /home/ubuntu/miniconda3/envs/python36/bin
command = metaeuk

[sepp]
path = /home/ubuntu/Applications/sepp/
command = run_sepp.py

运行界面

数据库下载：

busco v5

画图：
python scripts/generate_plot.py –wd my_summaries

'''
批量处理脚本：

cat id1|while read id 
do busco --config /public/home/fengting/config.ini -i $id.ort.fa -m protein -o $id 
done/

结果展示

结果展示

busco 结果解读：
C Complete 多少个BUSCO测试基因被覆盖。 C = S + D
S single-copy 多少个基因经过比对发现是单拷贝。 -
D duplicated 多少个基因经过比对发现包含多拷贝。 -
F Fragment 多少个基因经过比对覆盖不完全，只是部分比对上。 -
M Miss 没有得到比对结果的基因数 -
Total Total 总共测试的基因条目数 Total = C + F + M

参考链接：
config/config.ini · master · ezlab / busco · GitLab

BUSCO评估基因组组装和完整性 - (jianshu.com)

User guide BUSCO v5.3.2 (ezlab.org)

BUSCO - 组装质量评估 - (jianshu.com)