DNAharvester: A Nextflow Pipeline for Analysing Highly Degraded DNA from Ancient and Historical Specimens.

DNAharvester is a Nextflow pipeline that effectively processes highly degraded ancient and historical DNA, improving authentic data recovery and contamination mitigation.

• Why it matters: Analyzing ancient DNA is challenging due to short fragments, low endogenous content, damage, and contamination, which hinder accurate population genetic inferences and limit broader research access.
• What they did: The pipeline integrates metagenomic filtering, competitive mapping, adaptive aligner selection, and systematic bias evaluation, validated with simulated and empirical datasets, supporting various genomic analyses.
• The result: DNAharvester standardizes aDNA analysis, enhances reproducibility and portability, and makes genomic studies of ancient specimens more accessible to the research community.