Simulated Ancient DNA Reads for Human Chromosome 11 and Microbial Genomes

Simulated read data analyzed in a study on removing reference bias in ancient DNA analysis. The dataset includes all possible 50 bp reads overlapping chromosome 11 SNPs from the Human Origins dataset, with simulated post-mortem damage based on 102 ancient genomes. It also contains simulated microbial read data from reference genomes identified in an ancient Clovis genome.

Use Cases

• Benchmarking indel calling algorithms based on simulated ancient DNA reads.
• Testing methods for removing reference bias using reads carrying alternate or reference alleles.
• Evaluating sequence variation graph mapping tools on data with simulated post-mortem damage.
• Analyzing microbial community composition in ancient samples based on simulated microbial reads.

Strengths

• Simulated reads incorporate empirically estimated post-mortem damage patterns from 102 ancient genomes.
• Human data covers all possible 50 bp reads overlapping chromosome 11 SNPs in the Human Origins dataset.
• Includes both human sequence data and simulated microbial data from ancient reference genomes.

Limitations

• Row count and dataset size are unknown, which may limit suitability assessment.
• Column-level documentation is absent; field semantics must be inferred after download.
• Last update date is unknown; freshness unverified.

Provenance

Source

Rui Martiniano, University of Cambridge

Collection Method

Data was simulated using gargammel, with deamination added based on empirical damage estimates.