Genome Assesment - Lavadav/EPP531_AGA GitHub Wiki
6. BUSCO Analysis
BUSCO Slides
mkdir Busco
cd Busco
Symbolically link the fasta file to the current directory
mv <path to file.fasta> .
Check if BUSCO is loaded by singualirity
singularity exec -B $PWD /sphinx_local/images/ezlabgva-busco-v5.6.1_cv1.img busco --help
Run BUSCO
singularity exec -B $PWD /sphinx_local/images/ezlabgva-busco-v5.6.1_cv1.img busco -i Genome.fasta -m genome -l embryophyta -c 5 -o busco_results
7. Remove Mitochondria and Chloroplast genome from the assembly
mkdir MT_CP_removal
cd MT_CP_removal
spack load minimap2
Map your assembly to Chloroplast Genome
minimap2 -t 5 -x asm5 Chloroplast_genome.fasta assembly.fasta > Alignment.paf
Copy the following python scripts to the current directory
cp /pickett_sphinx/projects/EPP531_AGA/lyadav_EPPAGA/Busco/find_scaffolds_by_paf_coverage.py .
cp /pickett_sphinx/projects/EPP531_AGA/lyadav_EPPAGA/Busco/remove_contigs_by_name.py .
Find the list of mapping scaffolds
python3 find_scaffolds_by_paf_coverage.py Alignment.paf > Alignment_list.txt
Remove the mapping contigs
python remove_contigs_by_name.py Alignment_list.txt assembly.fasta
mv assembly.fasta assembly-CP_filtered.fasta