Hello,
I have created a custom database with 20 fungal genomes of the same genus by assigning specific Taxonomic IDs to each of them. I did not download any library from NCBI. Then, I denovo assembled 6 genomes belonging to the same species. But they are different strains. So I added the same taxonomic ID to each of the 6 Fasta files and added it to the library. Then, I ran the Kraken2 classification on the fastq reads. I know that there are reads that will hit at least 3-4 denovo-assembled genomes. But when I visualize the Kraken classification result, I do not see any differentiation in the amount of reads hitting the original species and the Denovo assembled species. All the hits show only one Genus e.g. Aspergillus.
Can you please suggest what should I do differently to find out the number of reads matching the genomes of my interest? At the moment, I just see 90% of the reads are assigned to a single Genus.
Thank you.
I think it would be easier for you to just map the reads with bwa-mem to a genome composed of all the fungal genomes. In order to use kraken2 you should create taxon ID for your de-novo assemblies, but I am not sure how to do that.