The Mexican government hosted a congressional meeting on September 12th, 2023 that involved displaying the purported bodies of two “non-human” specimens. Alongside the visual display of the specimens, there was a series of data published virtually including the following DNA Reads which seem to have been publishing around a year ago (July/August 2022):
1: https://www.ncbi.nlm.nih.gov/sra/PRJNA861322
2: https://www.ncbi.nlm.nih.gov/sra/PRJNA869134
3: https://www.ncbi.nlm.nih.gov/sra/PRJNA865375

These reads are quite large at 43 - 56.7 Gb each containing between 150.5G - 194.3G # of Bases. The data are listed with the following information at the NIH NCBI links:

1 ILLUMINA (HiSeq X Ten) run
Name: Ancient0002
Instrument: HiSeq X Ten
Strategy: WGS
Source: GENOMIC
Selection: RANDOM
Layout: PAIRED

Being outside of the field of genetics, I do not understand the context of the work that has been done around this data but have seen posts such as that by on r/bioinformatics by u/stackered in which deep skepticism is expressed and more importantly, suggested analyses are proposed.

I'm offering a bounty to help spur these analyses to be completed and would like to see the following questions addressed as recommended by u/stackered:

Check the quality of the reads
1. Checking with something like fastqc and other tools to check the quality and whether the reads were simulated or legitimate.
Conduct Basic Local Alignment Search Tool (BLAST) to search for the sequences in the reads against a large genomic database
1. Check for matches against known species
Run a microbial contaminant subtraction method
1. It is typical to see microbial contaminants added in the process or sample itself
Align the reads to the human reference genome (hg38) to compare the reads against the human genome
1. e.g. bowtie2 or other aligner
Assemble the DNA reads into contigs and scaffolds using de novo assembly methods

More information from u/stackered can be found in his original post in r/bioinformatics/

Answers