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--- benchmarking_universal_single-copy_orthologs_busco [2020/04/06 17:01] – 24.138.68.92
+++ benchmarking_universal_single-copy_orthologs_busco [2024/12/10 14:49] (current) – 129.173.94.151
@@ Line 1: / Line 1: @@
 **BUSCO: Benchmarking Universal Single-Copy Orthologs**
-Documentation by Sarah Shah and Dayana Salas-Leiva
+Documentation by Dayana Salas-Leiva (last update by Dandan Zhao 12-10-2024)
-Web:http://busco.ezlab.org/
+Web: http://busco.ezlab.org/ User Guide: https://busco.ezlab.org/busco_userguide.html
-You can check the completeness of your genome by picking out single-copy orthologs. **BUSCO** runs **tBLASTn**, **AUGUSTUS**, and **HMMER 3** based on single-copy orthologs from the **OrthoDB** database.
+You can check the completeness of your genome by identifying single-copy orthologs from the OrthoDB database. Newer versions of BUSCO utilize Metaeuk as a default gene predictor, can also be run with other tools like tBLASTn, AUGUSTUS, Prodigal, and HMMER3.
+tBLASTn for eukaryotic genome and prokaryotic transcriptome modes
+Augustus for eukaryotic genome mode
+Metaeuk for eukaryotic genome and eukaryotic transcriptome modes
+Prodigal for prokaryotic genome mode
+HMMER3 for all modes
+There are two main dataset versions of busco: odb9 (contains 303 orthologs only compatible with Busco3) and odb10 (contains 255 orthologous only compatible with Busco4)
 The following are examples of a shell script for genomic and a proteomic search:
-**** BUSCO 4.0.5 ****
+***  BUSCO 3 ***
+** Genomic: **
+   #!/bin/bash
+   #$ -S /bin/bash
+   ./etc/profile
+   #$ -pe threaded 1
+   #$ -cwd
+   cd $PWD
+   #busco3.0.0
+   source activate busco-3
+   export AUGUSTUS_CONFIG_PATH="/home/dsalas/Shared/BUSCO/config"
+   run_BUSCO.py -i <fasta_file> -o <output_dir_name> -l /home/dsalas/Shared/BUSCO/eukaryota_odb9 -m geno --cpu 1
+   conda deactivate
+** Proteomic: **
+   #!/bin/bash
+   #$ -S /bin/bash
+   ./etc/profile
+   #$ -pe threaded 1
+   #$ -cwd
+   cd $PWD
+   #busco3.0.0
+   source activate busco-3
+   export AUGUSTUS_CONFIG_PATH="/home/dsalas/Shared/BUSCO/config"
+   run_BUSCO.py -i <fasta_file> -o <output_dir_name> -l /home/dsalas/Shared/BUSCO/eukaryota_odb9 -m prot --cpu 1
+   conda deactivate
+** * BUSCO 4.0.5 * **
 ** Genomic: **
@@ Line 38: / Line 81: @@
-***  BUSCO 3 ***
+** * BUSCO 5.2.2 * **
-   #!/bin/bash
+** Genomic: default metaeuk**
-   #$ -S /bin/bash
-   ./etc/profile
+    source activate busco-5
-   #$ -pe threaded 3
+    INPUT='contigs_clean.fasta'
-   #$ -cwd
+    OUTDIR='busco5_out'
-   cd $PWD
+    MODE='genome'
-   #busco3.0.0
+    # setting the lineage db
-   source activate busco-3
+    ## the latest busco db for eukaryota is odb10
-   export AUGUSTUS_CONFIG_PATH="/home/dsalas/Shared/BUSCO/config"
+    LINEAGEDB='/scratch5/db/Eukfinder/BUSCO/busco_downloads/lineages/eukaryota_odb10/'
-   run_BUSCO.py -i fasta_file -o BUSCO_REF -l /home/dsalas/Shared/BUSCO/eukaryota_odb9 -m geno --cpu 3
+    ## busco v5 only works with odb10
-   conda deactivate
+    ## it will not work with odb9
+    # run busco
+    ## do not specify output dir with a trailing slash, it will lead to a fatal error
+    ## modes are genome, proteins, transcriptome
+    ## the below command will use Metaeuk as gene predictor
+    busco \
+        --in $INPUT \
+        --out $OUTDIR \
+        --mode $MODE \
+        --lineage_dataset $LINEAGEDB \
+        --cpu 8
+    conda deactivate
+** Proteomic:**
+    source activate busco-5
+    # in the busco-5 environment, AUGUSTUS_CONFIG_PATH is set to
+    # /scratch2/software/anaconda/envs/busco-5/config/
+    # but we don't have writing permissions there
+    # not sure why we need writing permissions but it doesnt work anyway
+    # but we copied that dir to a place where we do have writing permissions:
+    # you may want to copy it to your own home
+    export AUGUSTUS_CONFIG_PATH="$HOME/busco/config/"
+    INPUT='contigs_clean.fasta'
+    OUTDIR='busco5_contigs_clean_out'
+    MODE='genome'
+    AUGUSTUS_SPECIES='leishmania_tarentolae'
+    # setting the lineage db
+    ## the latest version (as of writing) is odb10
+    LINEAGEDB='/scratch5/db/Eukfinder/BUSCO/busco_downloads/lineages/eukaryota_odb10/'
+    ## busco v5 only works with odb10
+    ## it will not work with odb9
+    busco \
+        --in $INPUT \
+        --out $OUTDIR \
+        --mode $MODE \
+        --lineage_dataset $LINEAGEDB \
+        --cpu 8 \
+        --augustus \
+        --augustus_species $AUGUSTUS_SPECIES \
+    conda deactivate
 **Note**: Take out the mitochondrial genome before running this analysis.