Pooled contigs and raw reads

Hi Megan community,

I have pooled-contigs assembled through Megahit and the raw-reads per sample. No taxonomy or functions have been annotated. Can I continue my analysis in Megan? Could you give me an idea of how to do that?

This is my current workflow:
I was told to map my reads to the contig file using bowtie2. Then convert the output from .sam to .bam and .bam.bai. Now for the pooled-contigs, I was told to use DIAMOND to add function and taxonomy, obtain .daa file and meganize. Where I get lost is how to import the reads.bam and reads.bam.bai and contigs.megan - is this even possible?

Thank you.

Run the contains through the DIAMOND+MEGAN pipeline to assign taxonomy and function to your contigs. You can’t use your bam files in this process.