Hi there, I have just downloaded some genome assemblies from NCBI that are assembled at the contig level, and they are in .fna format. From what I understand, after assembly into contigs, the next step in a genome analysis workflow is mapping back to where the contigs fit on the genome. I am using bbmap to do this. However, bbmap needs 'reads' as input files as well, and my files only have the assembled contigs in the .fna file. Do I need to redownload the raw reads to feed into this input? Or am I not understanding this workflow properly..
Thank you!
Not quite. That mapping back is done only if you created the contigs yourself from raw sequence data. What exactly are you trying to do?