A tool to filter BUSCO output into files of single copy-sequences to be aligned for phylogenomics.
BUSCOfilter is a bash executable which runs in the Linux command line. The current version is up to date for BUSCO v5.7.1 output. Download the latest release, or use:
git clone https://github.com/Rowena-h/BUSCOfilter.git
| Option | Description |
|---|---|
| -h, --help | Display these options |
| -d, --directory | Directory containing BUSCO (>= v5.7.1) output folders which contain subdirectories with the typical run_ prefix. |
| -m, --mode | Set whether to produce files for all single-copy BUSCOs in the genomes or only those with a BUSCO in all genomes. Options all or common [Default = common] |
./BUSCOfilter -d /data/busco_folders -m all
In addition to a folder containing fasta files for each selected single copy BUSCO, the following files are produced when running BUSCOfilter:
| File | Description |
|---|---|
| genome_list | A list of the genomes 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 genomes. |
| busco_list | A list of IDs for the single copy BUSCOs that files were made for. If using -m all this will have a second column with the number of genomes that each BUSCO was found in. |
| error_list | If any of the BUSCO fasta files have the incorrect number of sequences when using -m common, the BUSCO IDs are stored in this file so that fasta files can be manually checked. |
If you use BUSCOfilter in your work please cite:
Hill R. (2024) BUSCOfilter. https://github.com/Rowena-h/BUSCOfilter