Extract mitochondrial contigs from draft contig-level genome using BLASTn

Question

[anna_shin]

Hi, I have some questions while studying Genome assembly.

Here's the dataset list I got : (1) NCBI mitochondrial reference genome (2) PacBio HiFi based contig-level assembly (my data) (3) Illumina short read (same sample with contig-level assembly data

I want to exclude overlapped mitochondrial contigs or noise using BLASTn.

I already run the blast with the following commands :

makeblastdb -in ${FASTA} -input_type fasta -dbtype nucl -out ${PREFIX}
blastn -query ${QRY} -task megablast -db ${PREFIX} -out ${QRY_PREFIX}_${PREFIX}.blast -outfmt 6 -num_threads 40 

And then what should I do next? Also, I want to know the criteria for Filtering

thank you,