I'm relatively new to bioinformatics, basically just working with fasta files and BLAST. I'm trying to run some comparisons of the human reference genome to population-specific reference genomes, as well as that of the neanderthal.
I have fasta files off Ensembl for the GRCh38, and I found a reference genome for Japanese individuals (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6555796/) as well as an Ashkenazi reference genome (https://github.com/AshkenaziGenome/Assembly/). I'm having trouble finding anything but BAM files for the neanderthal, and I can't find a reference genome at all for Sub-Saharan African populations.
My goal, as a newbie here, is to run some alignments and get some numbers supporting the notion that human diversity is low, and also that neanderthals fall outside our range.
I would be grateful for help finding some additional reference genomes, and fasta neanderthal chromosomes (or some way to convert from BAM). I know they are aDNA and very incomplete as well so I understand if the files I am looking for do not exist.
Thank you for the help! I am unfortunately tied to fasta and blast because I am trying to replicate someone else's methods to sus out the methodological errors.