Difference between revisions of "BUSCO"

Revision as of 22:26, 16 April 2020

Description

busco website

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

Required Modules

Serial

busco

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 /home/username/config.ini
$ export BUSCO_CONFIG_FILE=/home/username/config.ini
$ run_BUSCO.py

Datasets are located in /ufrc/data/reference/busco/

Available datasets:

arthropoda
bacteria
eukaryota
fungi
metazoa
vertebrata

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

$ ls /ufrc/data/reference/busco/

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.

Example

Let's copy aspergillus_nidulans

mkdir -p augustus/species

Load the busco module and copy augustus data

cp $AUGUSTUS_CONFIG_PATH/species/aspergillus_nidulans/ augustus/species/

Copy the models

cp $AUGUSTUS_CONFIG_PATH/model augustus/

Add

export AUGUSTUS_CONFIG_PATH=$(pwd)/augustus

to the busco job script and submit it.

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

@@ Line 35: / Line 35: @@
 -->
 ==System Variables==
-* HPC_{{#uppercase:{{#var:app}}}}_DIR - installation directory
+* HPC_{{uc:{{#var:app}}}}_DIR - installation directory
 <!--Configuration-->
 {{#if: {{#var: conf}}|==Configuration==
@@ Line 42: / Line 42: @@
 <!--Run-->
 {{#if: {{#var: exe}}|==Additional Information==
+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
+ $ export BUSCO_CONFIG_FILE=/home/username/config.ini
+ $ run_BUSCO.py
 Datasets are located in /ufrc/data/reference/busco/
@@ Line 53: / Line 60: @@
 *metazoa
 *vertebrata
+and many more. Run the following command to see all available species:
+ $ ls /ufrc/data/reference/busco/
+Example of busco run with metazoa dataset:
+ busco -f -in target.fa -o SAMPLE -l ${HPC_BUSCO_DAT}/metazoa -m genome
-Example of busco run with metazoa dataset:
+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.
-  busco -f -in target.fa -o SAMPLE -l metazoa -m genome
+;Example:
+Let's copy aspergillus_nidulans
+mkdir -p augustus/species
+* Load the busco module and copy augustus data
+ cp $AUGUSTUS_CONFIG_PATH/species/aspergillus_nidulans/ augustus/species/
+* Copy the models
+  cp $AUGUSTUS_CONFIG_PATH/model augustus/
-If you encounter an ''cannot write to to the Augustus config path'' error make sure you set the $AUGUSTUS_CONFIG_PATH variable as explained on the [[Augustus]] page.
+Add
+ export AUGUSTUS_CONFIG_PATH=$(pwd)/augustus
+to the busco job script and submit it.
 |}}
 <!--PBS scripts-->