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BUSCO: Benchmarking Universal Single-Copy Orthologs
Documentation by Dayana Salas-Leiva (last update 04-13-2020)
You can check the completeness of your genome by picking out single-copy orthologs. BUSCO runs tBLASTn, AUGUSTUS, and HMMER 3 based on single-copy orthologs from the OrthoDB database.
There are two main dataset versions of busco: odb9 (contains 303 orthologs only compatible with Busco3) and odb10 (contains 255 orthologous only compatible with Busco4)
The following are examples of a shell script for genomic and a proteomic search:
* BUSCO 3 *
Genomic:
#!/bin/bash #$ -S /bin/bash ./etc/profile #$ -pe threaded 1 #$ -cwd cd $PWD #busco3.0.0 source activate busco-3 export AUGUSTUS_CONFIG_PATH="/home/dsalas/Shared/BUSCO/config" run_BUSCO.py -i <fasta_file> -o <output_dir_name> -l /home/dsalas/Shared/BUSCO/eukaryota_odb9 -m geno --cpu 1 conda deactivate
Proteomic:
#!/bin/bash #$ -S /bin/bash ./etc/profile #$ -pe threaded 1 #$ -cwd cd $PWD #busco3.0.0 source activate busco-3 export AUGUSTUS_CONFIG_PATH="/home/dsalas/Shared/BUSCO/config" run_BUSCO.py -i <fasta_file> -o <output_dir_name> -l /home/dsalas/Shared/BUSCO/eukaryota_odb9 -m prot --cpu 1 conda deactivate
* BUSCO 4.0.5 *
Genomic:
#!/bin/bash #$ -S /bin/bash ./etc/profile #$ -pe threaded 1 #$ -cwd cd $PWD source activate busco #BUSCO 4.0.5 export AUGUSTUS_CONFIG_PATH="/home/dsalas/Shared/BUSCO/config" busco -i <input_scaffolds_file> -o <output_dir_name> -l /home/dsalas/Shared/BUSCO/eukaryota_odb9 -m geno --cpu 1
Proteomic:
#!/bin/bash #$ -S /bin/bash . /etc/profile #$ -pe threaded 1 #$ -cwd cd $PWD source activate busco #BUSCO 4.0.5 export AUGUSTUS_CONFIG_PATH="/home/dsalas/Shared/BUSCO/config" busco -i <predicted protein fasta> -o <output_dir-name> -l /home/dsalas/Shared/BUSCO/eukaryota_odb9 -m prot --cpu 1
Note: Take out the mitochondrial genome before running this analysis.
In the output folder:
-3 folders for the outputs of tBLASTn, AUGUSTUS, and HMMER, and a folder containing the single-copy BUSCO sequences. If you want to look into the details of the amino acid or nucleotide sequences that were predicted by AUGUSTUS and align them manually (for example, against a transcript contig), pick out the .faa or .fna files from the directory augustus_output/extracted_proteins
-“short summary” file showing how many BUSCO genes were found, how many were complete, fragmented, etc.
-“full table.tsv” showing a list of your contigs matched to BUSCO IDs.
-“missing busco list” showing a list of BUSCO genes that were not found in your genome.