Human Population Reference Genomes (+Neanderthal?)

Question

[emm008]

Hey everyone.

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!

Answer 1

[Matthias Zepper]

Well, of course these reference genomes do exist, but working with fasta files and BLAST is a completely unsuitable approach. Before searching any further reference genomes, please read up on the relevant scientific literature.

You can get some inspiration from the talk "Identifying admixture and ghost lineages in ancient genomes" by Tom van der Valk.

Also mind "African history – inferences from modern and ancient DNA" by Carina Schlebusch, if you are specifically interested in Sub-Saharan African populations. gnomAD also features some helpful tutorials.

[emm008]

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.