Hi, I have a metagenomics sample. I also have a set of reads from a genome. How can I pull similar or identical reads from the metagenomics sample? My ultimate goal is to reconstruct the genome hidden in the metagenomics sample.
How many are the reads from the genome that you already have?
If they are enough, you coud assemble them in contigs (or even to rough scaffolds of a genome) and then align against them.
If you have too few, the you could create a blast database or an aligner index and search against that.