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BUSCO stands for | 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. | |||
{{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. | |||
{{Commands | {{Commands | ||
|virtualenv ~/busco_env | |virtualenv ~/busco_env | ||
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}} | }} | ||
3. Install the wheel and its dependencies. | |||
{{Command | {{Command | ||
|prompt=(busco_env) $ | |prompt=(busco_env) $ | ||
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}} | }} | ||
4. Validate it. | |||
{{Command | {{Command | ||
|prompt=(busco_env) $ | |prompt=(busco_env) $ | ||
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==== Test ==== | ==== Test ==== | ||
7. Download a genome file. | |||
{{Commands | {{Commands | ||
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}} | }} | ||
'''8. | '''8. Run. | ||
Command to run a single genome: | Command to run a single genome: | ||
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===== Busco tips ===== | ===== Busco tips ===== | ||
Specify < | Specify <code>--in genome.fna</code> for single file analysis, | ||
Specify < | Specify <code>--in genome/</code> for multiple files analysis. | ||
===== Slurm tips ===== | ===== Slurm tips ===== | ||
Specify < | Specify <code>--offline</code> to avoid using the internet. | ||
Specify < | Specify <code>--cpu</code> to <code>$SLURM_CPUS_PER_TASK</code> in your job submission script to use the number of CPUs allocated. | ||
Specify < | 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> | |||
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. | |||
10.1. Activate your BUSCO virtual environment: | |||
{{Commands | {{Commands | ||
|source busco_env/bin/activate | |source busco_env/bin/activate | ||
}} | }} | ||
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 < | Make sure you have copied the config directory to a writable location and exported the <code>AUGUSTUS_CONFIG_PATH</code> variable. |