Difference between revisions of "BUSCO"

From UFRC
Jump to navigation Jump to search
 
(17 intermediate revisions by 3 users not shown)
Line 18: Line 18:
 
{{App_Description|app={{#var:app}}|url={{#var:url}}|name={{#var:app}}}}|}}
 
{{App_Description|app={{#var:app}}|url={{#var:url}}|name={{#var:app}}}}|}}
  
Assessing genome assembly and annotation completeness with Benchmarking Universal Single-Copy Orthologs
+
BUSCO stands for Assessing genome assembly and annotation completeness with Benchmarking Universal Single-Copy Orthologs
  
 
<!--Modules-->
 
<!--Modules-->
==Required Modules==
+
==Environment Modules==
 +
Run <code>module spider {{#var:app}}</code> to find out what environment modules are available for this application.
  
===Serial===
 
* {{#var:app}}
 
<!--
 
===Parallel (OpenMP)===
 
* intel
 
* {{#var:app}}
 
===Parallel (MPI)===
 
* intel
 
* openmpi
 
* {{#var:app}}
 
-->
 
 
==System Variables==
 
==System Variables==
* HPC_{{#uppercase:{{#var:app}}}}_DIR - installation directory
+
* HPC_{{uc:{{#var:app}}}}_DIR - installation directory
 
<!--Configuration-->
 
<!--Configuration-->
 
{{#if: {{#var: conf}}|==Configuration==
 
{{#if: {{#var: conf}}|==Configuration==
Line 45: Line 35:
 
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/busco
+
  $ cp $HPC_BUSCO_CONF/config.ini .
  $ export BUSCO_CONFIG_FILE=/home/username/busco
+
  $ export BUSCO_CONFIG_FILE=$(pwd)/config.ini
  $ run_BUSCO.py
+
  $ 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>
  
Datasets are located in /ufrc/data/reference/busco/
+
[https://busco.ezlab.org/busco_userguide.html#mandatory-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
  
Available datasets:
+
Datasets are located in /data/reference/busco/VERSION. The config.ini file is already configured to use the correct path.
 +
 
 +
'''Available datasets:'''
 +
<div style="column-count:3">
 
*arthropoda
 
*arthropoda
 
*bacteria
 
*bacteria
Line 60: Line 59:
 
*metazoa
 
*metazoa
 
*vertebrata  
 
*vertebrata  
and many more.
+
</div>
 +
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:
 
Example of busco run with metazoa dataset:
Line 67: Line 69:
 
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.
  
;Example:
+
<div class="mw-collapsible mw-collapsed" style="width:70%; padding: 5px; border: 1px solid gray;">
 
+
''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
  
* Load the busco module and copy augustus data
+
# Load the busco module and copy augustus data
cp $AUGUSTUS_CONFIG_PATH/species/aspergillus_nidulans/ augustus/species/
+
#*<pre>cp $AUGUSTUS_CONFIG_PATH/species/aspergillus_nidulans/ augustus/species/</pre>
* Copy the models
+
# Copy the models
cp $AUGUSTUS_CONFIG_PATH/models augustus/
+
#*<pre> cp $AUGUSTUS_CONFIG_PATH/model augustus/</pre>
 
+
#Add this to the busco job script and submit it.
Add
+
#*<pre>export AUGUSTUS_CONFIG_PATH=$(pwd)/augustus</pre></div></div>
export AUGUSTUS_CONFIG_PATH=$(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