Reproducible, portable, and efficient ancient genome reconstruction with nf-core/eager

Area of Science:

• Genomics
• Bioinformatics
• Archaeology

Background:

• Ancient DNA (aDNA) analysis is increasingly used across diverse scientific fields, leading to varied laboratory sizes and analytical scales.
• This heterogeneity necessitates adaptable and robust computational tools for processing aDNA data.

Purpose of the Study:

• To present an advanced, redesigned, and extended version of the EAGER pipeline for ancient genomic data analysis.
• To improve accessibility, adaptability, and reproducibility of aDNA analyses.
• To incorporate the latest routine practices in ancient genomics.

Main Methods:

• Development of a Nextflow pipeline, nf-core/eager.
• Focus on accessibility for various computing configurations.
• Emphasis on reproducibility for standardized analytical outcomes.
• Integration of current ancient genomic methodologies.

Main Results:

• A significantly enhanced and extended EAGER pipeline is now available.
• The pipeline is designed for improved accessibility and adaptability across different computational environments.
• nf-core/eager ensures high-quality software development and long-term maintenance support.

Conclusions:

• The nf-core/eager pipeline facilitates broader application of ancient DNA analyses by diverse research groups.
• It promotes robust analytical standards and incorporates up-to-date ancient genomic practices.
• This tool supports the growing needs of the ancient genomics field.