BUSCO/en: Difference between revisions

BUSCO stands for <i>Benchmarking sets of Universal Single-Copy Orthologs</i>. 

It is an application for assessing genome assembly and annotation completeness.

Recent versions are available as wheels. Older versions are available as a module, please see the module section below.

== Python Wheel ==

1. Load the necessary modules.

2. Create the virtual environment.

3. Install the wheel and its dependencies.

4. Validate it.

'''5.''' Freeze the environment and requirements set. For requirements text file usage, have a look at the bash submission script described in point number 8.

'''6.''' You must pre-download any datasets from [https://busco-data.ezlab.org/v5/data/ busco data] before submitting your job.

You have '''two''' options for datasets download:

 

===== Busco download command =====

'''6.1''' Use busco download command (preferred method). Here is one example:

 

It is also possible to do a bulk download by using the following arguments in place of the dataset name: "all", "prokaryota", "eukaryota", or "virus".

 

 

Directories hierarchy will look as follows:

 

Doing so, all your lineage files should be in '''busco_downloads/lineages/'''. When referring <code>--download_path busco_downloads/</code> in your busco command line, it will know where to find the lineage dataset argument <code>--lineage_dataset bacteria_odb10</code>. If the busco_download directory is not in your working directory, you would need to provide full path.

=====Wget download command =====

All files must be decompressed: <code>tar -xvf file.tar.gz</code>

7. Download a genome file.

'''8. Run.

Command to run multiple genomes that would be saved in the '''genome/''' directory: (As describe here, genome folder would need to be in the current directory or you would need to provide the full path).

===== Busco tips =====

Specify <code>--in genome.fna</code> for single file analysis,

9. For advanced users who want to use Augustus parameters: <code>--augustus_parameters="--yourAugustusParameter".</code>

Copy the Augustus config directory to a writable location:

Make sure to define the <code>AUGUSTUS_CONFIG_PATH</code> environment variable:

10. To use SEPP parameters, you need to install SEPP locally in your virtual environment. This should be done in a login node.

10.1. Activate your BUSCO virtual environment:

10.2. Install dendropy:

'''10.3.''' Install SEPP:

'''10.4.''' Validate the installation:

'''10.5.''' When using SEPP, because it is installed locally you cannot create the virtual environment as we have described in previous submission script demo. You simply need to add this command which activates your local virtual environment just after the loading module command line:

|content=This section is outdated. We are currently working on updating it.

'''1.''' Load the necessary modules:

This will also load modules for <code>augustus, blast+, hmmer</code> and some other

'''2.''' Copy the configuration file:

'''3.''' Edit the configuration file. The locations of external tools are all specified in the last section, which is shown below:

'''4.''' Copy the Augustus config directory to a writable location:

'''5.''' Check that it runs.

Make sure you have copied the config directory to a writable location and exported the <code>AUGUSTUS_CONFIG_PATH</code> variable.