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BUSCO

http://busco.ezlab.org/

INSTALL Augustus

cd $HOME
curl -O http://augustus.gobics.de/binaries/augustus.2.5.5.tar.gz
tar -zxf augustus.2.5.5.tar.gz
cd augustus.2.5.5/
make
export PATH=$PATH:$(pwd)/bin
export AUGUSTUS_CONFIG_PATH=$(pwd)/config

INSTALL BUSCO:

Some new system software is required:

sudo -y apt-get install ncbi-blast+ hmmer

Now, install BUSCO:

cd $HOME
curl -O http://busco.ezlab.org/files/BUSCO_v1.1b1.tar.gz
tar -zxf BUSCO_v1.1b1.tar.gz
cd BUSCO_v1.1b1/
export PATH=$PATH:$(pwd)

Go to assembly directory and download BUSCO reference: BUSCO reference needs to be in same DIR as where you are going to run BUSCO.

cd /mnt/assembly/ #or wherever your assemblies are
curl -LO https://www.dropbox.com/s/o8roa5ayt5dbnl4/bacteria_busco.tar.gz
tar -zxf bacteria_busco.tar.gz

Run BUSCO for assemblies: There are Eukaryote, Metazoa, Arthropod, Vertebrate, Plant referneces for use with other genomes.

python3 /home/ubuntu/BUSCO_v1.1b1/BUSCO_v1.1b1.py -f \
   -m genome -in megahit-assembly.fa \
   --cpu 8 -l bacteria -o megahit
python3 /home/ubuntu/BUSCO_v1.1b1/BUSCO_v1.1b1.py -f \
   -m genome -in spades-assembly.fa \
   --cpu 8 -l bacteria -o spades -f

Results for SPAdes vs. Velvet vs. Reference

Run:

cat run*/short*