A tool to filter BUSCO output into folders of common single copy sequences to be aligned for phylogenomics.
BUSCOfilter is a bash script which runs in the Linux command line. To download, simply use:
git clone https://github.com/Rowena-h/BUSCOfilter.git
Make the script executable with:
chmod +x BUSCOfilter
Option | Description |
---|---|
-h, --help | Display these options |
-d, --directory | Directory containing busco output folders which must have the typical 'run_' prefix |
./BUSCOfilter -d /data/busco_folders
In addition to a folder containing fasta files for each selected single copy BUSCO, the following files are produced when running BUSCOfilter:
File | Description |
---|---|
assembly_list | A list of the assemblies found in the provided directory (i.e. the name of each BUSCO output folder after the 'run_' prefix) |
busco_stats | A tabular summary of the BUSCO run statistics for all the provided assemblies |
busco_list | A list of IDs for the single copy BUSCOs that are found in all assemblies |
error_list | If there is a problem in producing any of the fasta files, the BUSCO IDs are stored in this file so that fasta files can be manually checked |