Difference between revisions of "BUSCO"

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{{App_Description|app={{#var:app}}|url={{#var:url}}|name={{#var:app}}}}|}}
 
{{App_Description|app={{#var:app}}|url={{#var:url}}|name={{#var:app}}}}|}}
  
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Assessing genome assembly and annotation completeness with Benchmarking Universal Single-Copy Orthologs
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BUSCO stands for Assessing genome assembly and annotation completeness with Benchmarking Universal Single-Copy Orthologs
  
 
<!--Modules-->
 
<!--Modules-->
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==Required Modules==
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==Environment Modules==
 +
Run <code>module spider {{#var:app}}</code> to find out what environment modules are available for this application.
  
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===Serial===
 
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* {{#var:app}}
 
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<!--
 
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===Parallel (OpenMP)===
 
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* intel
 
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* {{#var:app}}
 
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===Parallel (MPI)===
 
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* intel
 
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* openmpi
 
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* {{#var:app}}
 
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-->
 
 
==System Variables==
 
==System Variables==
 
* HPC_{{uc:{{#var:app}}}}_DIR - installation directory
 
* HPC_{{uc:{{#var:app}}}}_DIR - installation directory
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Busco uses a config file which needs to be copied and modified to your needs.  
 
Busco uses a config file which needs to be copied and modified to your needs.  
  
−
  $ cp $HPC_BUSCO_CONF/config.ini /home/username/config.ini
+
  $ cp $HPC_BUSCO_CONF/config.ini .
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  $ export BUSCO_CONFIG_FILE=/home/username/config.ini
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  $ export BUSCO_CONFIG_FILE=$(pwd)/config.ini
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  $ busco -i ... <other arguments>
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  $ busco -f -i ... <other arguments>
 +
 
 +
If you don't need to modify the config file you can use the installed copy:
 +
$ busco -f --config ${HPC_BUSCO_CONF}/config.ini -i ... <other arguments>
  
 
[https://busco.ezlab.org/busco_userguide.html#mandatory-arguments Mandatory arguments]
 
[https://busco.ezlab.org/busco_userguide.html#mandatory-arguments Mandatory arguments]
  
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-i or --in defines the input file to analyse which is either a nucleotide fasta file or a protein fasta file, depending on the BUSCO mode. As of v5.1.0 the input argument can now also be a directory containing fasta files to run in batch mode.
+
*-i or --in defines the input file to analyse which is either a nucleotide fasta file or a protein fasta file, depending on the BUSCO mode. As of v5.1.0 the input argument can now also be a directory containing fasta files to run in batch mode.
−
 
+
*-o or --out defines the folder that will contain all results, logs, and intermediate data
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-o or --out defines the folder that will contain all results, logs, and intermediate data
+
*-m or --mode sets the assessment MODE: genome, proteins, transcriptome
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*-l or --lineage_dataset
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-m or --mode sets the assessment MODE: genome, proteins, transcriptome
 
−
 
 
−
-l or --lineage_dataset
 
  
 
Datasets are located in /data/reference/busco/VERSION. The config.ini file is already configured to use the correct path.
 
Datasets are located in /data/reference/busco/VERSION. The config.ini file is already configured to use the correct path.
  
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'''Available datasets:'''
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Available datasets:
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<div style="column-count:3">
 
*arthropoda
 
*arthropoda
 
*bacteria
 
*bacteria
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*metazoa
 
*metazoa
 
*vertebrata  
 
*vertebrata  
 +
</div>
 
and many more. Run the following command to see all available species:
 
and many more. Run the following command to see all available species:
 
  $ ls /data/reference/busco/VERSION
 
  $ ls /data/reference/busco/VERSION
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e.g.
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  #for example: $ ls /data/reference/busco/v5
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  $ ls /data/reference/busco/v5
 
  
 
Example of busco run with metazoa dataset:
 
Example of busco run with metazoa dataset:
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To allow busco to retrain an existing Augustus dataset create a local copy of the data and set $AUGUSTUS_CONFIG_PATH variable to that path as explained on the [[Augustus]] page.
 
To allow busco to retrain an existing Augustus dataset create a local copy of the data and set $AUGUSTUS_CONFIG_PATH variable to that path as explained on the [[Augustus]] page.
  
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;Example:
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<div class="mw-collapsible mw-collapsed" style="width:70%; padding: 5px; border: 1px solid gray;">
−
 
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''Expand this section to view an example, copying aspergillus nidulans.''
 +
<div class="mw-collapsible-content" style="padding: 5px;">
 
Let's copy aspergillus_nidulans
 
Let's copy aspergillus_nidulans
  
 
mkdir -p augustus/species
 
mkdir -p augustus/species
  
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* Load the busco module and copy augustus data
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# Load the busco module and copy augustus data
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cp $AUGUSTUS_CONFIG_PATH/species/aspergillus_nidulans/ augustus/species/
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#*<pre>cp $AUGUSTUS_CONFIG_PATH/species/aspergillus_nidulans/ augustus/species/</pre>
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* Copy the models
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# Copy the models
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cp $AUGUSTUS_CONFIG_PATH/model augustus/
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#*<pre> cp $AUGUSTUS_CONFIG_PATH/model augustus/</pre>
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+
#Add this to the busco job script and submit it.
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Add
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#*<pre>export AUGUSTUS_CONFIG_PATH=$(pwd)/augustus</pre></div></div>
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export AUGUSTUS_CONFIG_PATH=$(pwd)/augustus
 
−
to the busco job script and submit it.
 
 
|}}
 
|}}
 
<!--PBS scripts-->
 
<!--PBS scripts-->

Latest revision as of 19:38, 27 March 2023

Description

busco website  

BUSCO stands for Assessing genome assembly and annotation completeness with Benchmarking Universal Single-Copy Orthologs

Environment Modules

Run module spider busco to find out what environment modules are available for this application.

System Variables

  • HPC_BUSCO_DIR - installation directory

Additional Information

Busco uses a config file which needs to be copied and modified to your needs. 

$ cp $HPC_BUSCO_CONF/config.ini .
$ export BUSCO_CONFIG_FILE=$(pwd)/config.ini
$ busco -f -i ... <other arguments>

If you don't need to modify the config file you can use the installed copy: 

$ busco -f --config ${HPC_BUSCO_CONF}/config.ini -i ... <other arguments>

Mandatory arguments

  • -i or --in defines the input file to analyse which is either a nucleotide fasta file or a protein fasta file, depending on the BUSCO mode. As of v5.1.0 the input argument can now also be a directory containing fasta files to run in batch mode.
  • -o or --out defines the folder that will contain all results, logs, and intermediate data
  • -m or --mode sets the assessment MODE: genome, proteins, transcriptome
  • -l or --lineage_dataset

Datasets are located in /data/reference/busco/VERSION. The config.ini file is already configured to use the correct path.

Available datasets:

  • arthropoda
  • bacteria
  • eukaryota
  • fungi
  • metazoa
  • vertebrata

and many more. Run the following command to see all available species: 

$ ls /data/reference/busco/VERSION
#for example: $ ls /data/reference/busco/v5

Example of busco run with metazoa dataset: 

busco -f -in target.fa -o SAMPLE -l ${HPC_BUSCO_DAT}/metazoa -m genome

To allow busco to retrain an existing Augustus dataset create a local copy of the data and set $AUGUSTUS_CONFIG_PATH variable to that path as explained on the Augustus page.

Expand this section to view an example, copying aspergillus nidulans.

Let's copy aspergillus_nidulans

mkdir -p augustus/species

  1. Load the busco module and copy augustus data 
    • cp $AUGUSTUS_CONFIG_PATH/species/aspergillus_nidulans/ augustus/species/
  2. Copy the models 
    •  cp $AUGUSTUS_CONFIG_PATH/model augustus/
  3. Add this to the busco job script and submit it. 
    • export AUGUSTUS_CONFIG_PATH=$(pwd)/augustus



Citation

If you publish research that uses busco you have to cite it as follows:

BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs. Felipe A. Simão, Robert M. Waterhouse, Panagiotis Ioannidis, Evgenia V. Kriventseva, and Evgeny M. Zdobnov Bioinformatics, published online June 9, 2015


Retrieved from "https://help.rc.ufl.edu/mediawiki/index.php?title=BUSCO&oldid=27703"