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buscofilter's Introduction

BUSCOfilter

A tool to filter BUSCO output into folders of common single copy sequences to be aligned for phylogenomics.

Requirements

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

Usage

Option Description
-h, --help Display these options
-d, --directory Directory containing busco output folders which must have the typical 'run_' prefix

Example

./BUSCOfilter -d /data/busco_folders

Output

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

buscofilter's People

Contributors

rowena-h avatar

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