Hi,
It is known that the size of the database affects competitive mapping tools like Bowtie2. So, should I map metagenomic sequences to a single genome with the prophage region, or should I map the sequences to a large database with multiple genomes (like GTDB) and specify the prophage coordinates for interesting genomes?
Hi,
It is known that the size of the database affects competitive mapping tools like Bowtie2. So, should I map metagenomic sequences to a single genome with the prophage region, or should I map the sequences to a large database with multiple genomes (like GTDB) and specify the prophage coordinates for interesting genomes?