Illumina NovaSeq 6000 paired end sequencing
Reads processed via nf-core/eager v2.4.1. Aligned to human reference g1k v37 decoy using BWA aln (-n 0.01, -k 2, -l 1024). BAM files filtered (MQ � 25, length � 30bp) and deduplicated (DeDup v0.12.8). Post-alignment damage trimming performed using bamUtil trimBam (v1.0.15), clipping 2bp from both ends of the fragments to account for ancient DNA deamination patterns.
Double-stranded libraries prepared following Meyer & Kircher (2010) with partial UDG treatment according to Rohland et al. (2015). Target enrichment performed via in-solution hybridization using the myBaits Expert Human Affinities Kit �Prime Plus�.