• 软件安装及测试
  • 安装方法
  • 小测试数据下载
• 软件参数

介绍

BUSCO软件可以对基因组，注释结果进行质量评估，作者目前已经更新到了v5版本。BUSCO软件根据OrthoDB数据库，构建了几个大的进化分支的单拷贝基因集，该基因集在对应分类集合上理论上保守且仅有一个拷贝。将基因组/蛋白序列与该基因集进行比较，根据比对上的比例、完整性，来评价拼接结果的准确性和完整性。

仓库地址: https://busco.ezlab.org/busco_userguide.html
cite: Seppey M., Manni M., Zdobnov E.M. (2019) BUSCO: Assessing Genome Assembly and Annotation Completeness. In: Kollmar M. (eds) Gene Prediction. Methods in Molecular Biology, vol 1962. Humana, New York, NY. 2019 doi.org/10.1007/978-1-4939-9173-0_14. PMID:31020564

软件安装及测试

安装方法

直接拉取 docker镜像（推荐）

docker pull ezlabgva/busco:v5.0.0_cv1

小测试数据下载

下载酿酒酵母基因组

 https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/146/045/GCF_000146045.2_R64/GCF_000146045.2_R64_genomic.fna.gz
 gzip -d GCF_000146045.2_R64_genomic.fna.gz

通过镜像打开容器

 docker run -ti --rm --user $(id -u) -v $PWD:/busco_wd ezlabgva/busco:v5.0.0_cv1  bash

由于v4以上版本引入了自动odb库选择和下载，直接使用基因组文件作为输入

 busco --in GCF_000146045.2_R64_genomic.fna --mode genome --out tmp -f

弹出的info显示自动选择的库存在问题

INFO: Downloading file 'https://busco-data.ezlab.org/v5/data/lineages/archaea_odb10.2021-02-23.tar.gz'

下载的是古菌的库archaea_odb10，似乎不大对劲。指定自动发现真核生物相关库的参数--auto-lineage-euk

 busco --in GCF_000146045.2_R64_genomic.fna --mode genome --out tmp -f --auto-lineage-euk

下载了真核生物的库，但通过 busco --list-datasets 命令可以看到其实有更接近的库 --> saccharomycetes_odb10 。看起来这个自动判断不大靠谱的样子。

手动下载saccharomycetes_odb10数据库,解压后放到指定目录，在命令指定该目录位置，注意镜像中位置由于挂载可能存在变化

 busco -i GCF_000146045.2_R64_genomic.fna -l saccharomycetes_odb10 --download_path busco_downloads -o tmp -m genome -f --offline -c 10

odb库下载: https://busco-data.ezlab.org/v5/data/lineages/

软件参数

  -i FASTA FILE, --in FASTA FILE
                        Input sequence file in FASTA format. Can be an assembled genome or transcriptome (DNA), or protein sequences from an annotated gene set.
  -o OUTPUT, --out OUTPUT
                        Give your analysis run a recognisable short name. Output folders and files will be labelled with this name. WARNING: do not provide a path
  -m MODE, --mode MODE  Specify which BUSCO analysis mode to run.
                        There are three valid modes:
                        - geno or genome, for genome assemblies (DNA)
                        - tran or transcriptome, for transcriptome assemblies (DNA)
                        - prot or proteins, for annotated gene sets (protein)
  -l LINEAGE, --lineage_dataset LINEAGE
                        Specify the name of the BUSCO lineage to be used.
  --auto-lineage        Run auto-lineage to find optimum lineage path
  --auto-lineage-prok   Run auto-lineage just on non-eukaryote trees to find optimum lineage path
  --auto-lineage-euk    Run auto-placement just on eukaryote tree to find optimum lineage path
  -c N, --cpu N         Specify the number (N=integer) of threads/cores to use.
  -f, --force           Force rewriting of existing files. Must be used when output files with the provided name already exist.
  -r, --restart         Continue a run that had already partially completed.
  -q, --quiet           Disable the info logs, displays only errors
  --out_path OUTPUT_PATH
                        Optional location for results folder, excluding results folder name. Default is current working directory.
  --download_path DOWNLOAD_PATH
                        Specify local filepath for storing BUSCO dataset downloads
  --datasets_version DATASETS_VERSION
                        Specify the version of BUSCO datasets, e.g. odb10
  --download_base_url DOWNLOAD_BASE_URL
                        Set the url to the remote BUSCO dataset location
  --update-data         Download and replace with last versions all lineages datasets and files necessary to their automated selection
  --offline             To indicate that BUSCO cannot attempt to download files
  --metaeuk_parameters METAEUK_PARAMETERS
                        Pass additional arguments to Metaeuk for the first run. All arguments should be contained within a single pair of quotation marks, separated by commas. E.g. "--param1=1,--param2=2"
  --metaeuk_rerun_parameters METAEUK_RERUN_PARAMETERS
                        Pass additional arguments to Metaeuk for the second run. All arguments should be contained within a single pair of quotation marks, separated by commas. E.g. "--param1=1,--param2=2"
  -e N, --evalue N      E-value cutoff for BLAST searches. Allowed formats, 0.001 or 1e-03 (Default: 1e-03)
  --limit REGION_LIMIT  How many candidate regions (contig or transcript) to consider per BUSCO (default: 3)
  --augustus            Use augustus gene predictor for eukaryote runs
  --augustus_parameters AUGUSTUS_PARAMETERS
                        Pass additional arguments to Augustus. All arguments should be contained within a single pair of quotation marks, separated by commas. E.g. "--param1=1,--param2=2"
  --augustus_species AUGUSTUS_SPECIES
                        Specify a species for Augustus training.
  --long                Optimization Augustus self-training mode (Default: Off); adds considerably to the run time, but can improve results for some non-model organisms
  --config CONFIG_FILE  Provide a config file
  -v, --version         Show this version and exit
  -h, --help            Show this help message and exit
  --list-datasets       Print the list of available BUSCO datasets