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BUSCO and QUAST
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BUSCO and QUAST
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### BUSCO as a quality analysis tool using packages of sequencies to compare how complete your Assemblie is
### QUAST use the
###############################################################################################################################################################################################################
### AS ALWAYS YOU HAVE 2 WAYS TO DOWNLOAD, FIRST IN CONDA AND SECOND IN SERVE
### 1 OPTION - see ANACONDA, MINICONDA & CONDA file
### as the others programms, make a envoirment in conda
(base) $ conda create -n BUSCO
(base) $ conda activate BUSCO
(BUSCO) $ conda install bioconda::BUSCO
### DOWNLOAD A LOT OF THINGS
### 2 OPTION
### Install in default terms
### There is more componets to install to make BUSCO works like : BioPython (https://biopython.org/) | Pandas (https://pandas.pydata.org/) | BBMAP (https://jgi.doe.gov/data-and-tools/software-tools/bbtools/)
### tBLASTn 2.2 | Augustus 3.2 (https://bioinf.uni-greifswald.de/augustus/) | Metauek (https://github.com/soedinglab/metaeuk) | Prodigal (https://github.com/hyattpd/Prodigal) | HMMER3.1 (http://hmmer.org/) |
### SEPP (https://github.com/smirarab/sepp/) | R and ggplot2
(base) $ git clone https://gitlab.com/ezlab/busco.git
(base) $ cd busco/
### HOW TO USE WITH CONDA
(BUSCO) $ busco -i <fasta_file> -m <mode> -o <folder_name> -c <numeber_of_cores> -l <lineage> -
### -i the fasta file can be genomic or protein and -m you define the mode of the file "genome", "protein", "trasncriptome"
### -o output folder name would like to have. To check the lineages = busco --list-datasets
(base) $ conda activate BUSCO
### check the catalog/list of lineages or the full available datasets
(BUSCO) $ busco --lineages_datasets ; busco --list-dataset
(BUSCO) $ busco -i Actino_*.fna -m genome -o Busco_Actino -c 8 -l actinopterygii_odb10
### OR
(BUSCO) $ busco -i Sarco_*.fna -m genome -o Busco_Sarco -c 8 -l tetrapoda_odb10
### OR
(BUSCO) $ busco -i Actino_*.fna Sarco_*.fna -m genome -o Busco_Ostei -c 8 -l vertebrata_odb10
### exemple of protain mode
(BUSCO) $ busco -i Actino_*_prot.faa -m protein -o Busco_Actino -c 8 -l actinopterygii_odb10
### Separate, or copy, all *.txt
(BUSCO) $ for file in Busco_[AS]*.fna
do cd $file ; mv *.txt ~/PATH/; cd ..
done
(BUSCO) $ for file in Busco_[AS]*.fna
do cd $file ; cp *.txt ~/PATH/; cd ..
done
### After busco run, alocate all *.txt inside each directory output to other place and use the command phyton3 to create the figure
### Use in the directory with all *.txt files
(BUSCO) $ python3 ~/miniconda3/envs/busco/bin/generate_plot.py -wd busco_actino
### -wd working directory the figures will be
###############################################################################################################################################################################################################
### 2 ways to dowloand quast
### 1 OPTION - see ANACONDA, MINICONDA & CONDA file
(base) $ conda creat -n QUAST
(base) $ conda activate QUAST
(QUAST) $ conda install bioconda::QUAST
(QUAST) $ conda update
### DOWNLOAD A LOT OF THINGS
### 2 OPTION
### There are some limits to use the tool. In the manual "slightly limited functionality: BUSCO is not working there."
###
(base) $ wget https://github.com/ablab/quast/releases/download/quast_5.2.0/quast-5.2.0.tar.gz
(base) $ tar -xzfv quast-5.2.0.tar.gz
(base) $ cd quast-5.2.0
### HOW TO USE WITH CONDA
(QUAST) $ python quast.py <commands> <contig_file(s)>
(QUAST) $