BUSCO/en: Difference between revisions

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BUSCO stands for "Benchmarking sets of Universal Single-Copy Orthologs".   
BUSCO stands for <i>Benchmarking sets of Universal Single-Copy Orthologs</i>.   
It is an application for assessing genome assembly and annotation completeness.
It is an application for assessing genome assembly and annotation completeness.


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


To see the latest available version, run:
To see the latest available version, run
{{Command|avail_wheel busco}}
{{Command|avail_wheel busco}}


== Python Wheel ==
== Python Wheel ==
=== Installation ===
=== Installation ===
'''1.''' Load the necessary modules:
1. Load the necessary modules.
{{Commands
{{Commands
|module load StdEnv/2020 gcc python/3.10 augustus hmmer blast+ metaeuk prodigal r bbmap}}
|module load StdEnv/2020 gcc python/3.10 augustus hmmer blast+ metaeuk prodigal r bbmap}}


'''2.''' Create the virtual environment:
2. Create the virtual environment.
{{Commands
{{Commands
|virtualenv ~/busco_env
|virtualenv ~/busco_env
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}}
}}


'''3.''' Install the wheel and its dependencies:
3. Install the wheel and its dependencies.
{{Command
{{Command
|prompt=(busco_env) $
|prompt=(busco_env) $
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}}
}}


'''4.''' Validate it:
4. Validate it.
{{Command
{{Command
|prompt=(busco_env) $
|prompt=(busco_env) $
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==== Test ====
==== Test ====
'''7.''' Download a genome file.
7. Download a genome file.


{{Commands
{{Commands
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}}
}}


'''8.''' Run:
'''8. Run.


Command to run a single genome:
Command to run a single genome:
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===== Busco tips =====
===== Busco tips =====


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


Specify <tt>--in genome/</tt> for multiple files analysis.
Specify <code>--in genome/</code> for multiple files analysis.


===== Slurm tips =====
===== Slurm tips =====
Specify <tt>--offline</tt> to avoid using the internet.
Specify <code>--offline</code> to avoid using the internet.


Specify <tt>--cpu</tt> to <tt>$SLURM_CPUS_PER_TASK</tt> in your job submission script to use the number of CPUs allocated.
Specify <code>--cpu</code> to <code>$SLURM_CPUS_PER_TASK</code> in your job submission script to use the number of CPUs allocated.


Specify <tt>--restart</tt> to restart from a partial run.
Specify <code>--restart</code> to restart from a partial run.


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


Copy the Augustus config directory to a writable location:
Copy the Augustus config directory to a writable location:
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====SEPP parameters====
====SEPP parameters====
'''10.''' To use SEPP parameters, you need to install SEPP locally in your virtual environment. This should be done in a login node.
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:
10.1. Activate your BUSCO virtual environment:
{{Commands
{{Commands
|source busco_env/bin/activate
|source busco_env/bin/activate
}}
}}


'''10.2.''' Install dendropy:
10.2. Install dendropy:
{{Commands
{{Commands
|pip install 'dendropy<4.6'
|pip install 'dendropy<4.6'
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|source ~/busco_env/bin/activate
|source ~/busco_env/bin/activate
}}
}}




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= Troubleshooting =
= Troubleshooting =
== Cannot write to Augustus config path ==
== Cannot write to Augustus config path ==
Make sure you have copied the config directory to a writable location and exported the <tt>AUGUSTUS_CONFIG_PATH</tt> variable.
Make sure you have copied the config directory to a writable location and exported the <code>AUGUSTUS_CONFIG_PATH</code> variable.
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