Genome-wide ancient DNA data from two 7,000-year-old individuals from Takarkori Rockshelter in Libya, and Archaic admixture capture data from seven 15,000-year-old individuals from Taforalt Cave, Morocco.

Screening data for libraries created in this study (TKH001.A0101 from TKH001, and XXX001.A18276 and XXX001.A18277 from TKH009) were obtained through shallow shotgun sequencing. SNP enrichment was performed using three capture sets: the 1240k and Twist panels for population genetic analyses, and the Archaic Admixture panel for investigating archaic ancestry. All capture data presented here were aligned to the human reference genome (hg19, GRCh37), filtered for PCR duplicates, filtered for mapping quality of 25 and a minimum length of 30 base pairs. The shallow shotgun data was processed similarly, except with a mapping quality threshold of 30. Additionally, Archaic Admixture capture data were generated from 22 previously existing libraries (van de Loosdrecht et al., 2018) derived from seven Taforalt individuals (TAF09, TAF010, TAF011, TAF012, TAF13, TAF014, TAF015). We provide BAM files from these libraries, aligned to the human reference genome (hg19, GRCh37) and filtered for PCR duplicates. Merged data for each individual, processed analogously to the Takarkori data, are also included.