Bowtie2 reference help

[Niranjanks]

Hi there I am working on paired-end Illumina 2500 data and I wish to check for chloroplast and mitochondrial DNA contamination in it.

My Illumina data is around 1 Gigabases and I have the whole chloroplast genome and also mitochondrial DNA contigs.

My question is -

Will my reference here for bowtie2 for which I have to make the Index be the chloroplast or mitochondrial DNA OR will it be the paired end Illumina data? I am talking about the -x command in bowtie2

I want to compare them so I can remove contaminant chloroplast/mitochondrial DNA.

I was thinking about making the paired end Illumina data as my reference index and then align the relatively shorter chloroplast DNA/ mitochondrial DNA contigs to it. However I have no idea how to make a reference of paired end data even after reading the manual.

Please advise.
Thank you.

[Niranjanks]

Found the answer.

Make a multi fasta file combining the choloroplast and mitochondrial DNA and use it as an index.

Alternatively can just keep the unmapped reads to filter out the contamination.