Extract mitogenome from seqences

Question

[harmadikemil]

Dear All!

I have a big database, full of different sequences, most of it in fastq.gz files. (archaic and recent human sequences) My task is to extract the mitogenome sequences from them and reconstruct the mitogenome in one fasta. I have tried to map to MT ref genome, and remove all unmapped reads, and from that convert the reads into one fasta, but it's still not good. Any idea how i can filter it out? (I need it to determine the haplogroups). The fastq-s are various sizes, from a few thousand reads to whole genome.

Thank you in advance

[GenoMax]

My task is to extract the mitogenome sequences from them and reconstruct the mitogenome in one fasta.

You want to create a mitochondrial genome for each of your sequence files independently, correct?

I have tried to map to MT ref genome, and remove all unmapped reads, and from that convert the reads into one fasta, but it's still not good

So if you have a BAM alignment file (with MT reference) for each sample, you can create a new consensus using these directions: Generating consensus sequence from bam file.

Any idea how i can filter it out?

Filter what out?