pastForward: a Snakemake pipeline for ancient and historical DNA with eukaryote-wide taxonomic screening and tracking of copy-number variation
Ancient and historical DNA has the potential to resolve many open questions in biology. While pipelines for processing ancient and historical DNA exist, none combine user-friendly, configurable processing with copy number variation tracking and targeted taxonomic profiling. Therefore, we developed pastForward, a fully automated Snakemake pipeline that integrates all analysis steps from raw reads…
PastForward is a fully automated Snakemake pipeline designed to streamline the processing of ancient and historical DNA data. This pipeline incorporates user-friendly features, copy number variation tracking, and targeted taxonomic profiling, which are often lacking in existing pipelines. The integration of pastForward into an analysis workflow allows for the seamless transformation of raw reads into damage-rescaled BAM files, ensuring reproducibility throughout the process.
Key features of pastForward include adapter trimming, read merging, deduplication, damage assessment, and quality rescaling, resulting in an interactive report summarizing endogenous read content, library complexity, and coverage statistics. These reports enable quick assessment of sequencing data quality.
The pipeline supports both single- and paired-end NGS libraries and can map to multiple reference sequences, facilitating co-analysis of host and endosymbiont sequences. This capability is particularly useful for genotyping marker genes, such as COI.
Two novel tools are integrated into pastForward: ECMSD (Efficient Comprehensive Mitochondrial Sequence Detector) and REVEAL (Read-based Estimation and Visualization of Element Abundance and Loci). ECMSD screens each library for eukaryotic DNA by aligning reads against a mitochondrial reference database, detecting bacteria, archaea, and viruses using Centrifuge. REVEAL quantifies and visualizes copy number variation of genetic features, such as transposable elements or gene duplications.
To demonstrate the pipeline's capabilities, two case studies are presented. First, pastForward is applied to dog genomic time series, including Neolithic samples, confirming an increase in the copy number of AMY2B during domestication. Second, historical Drosophila melanogaster genomes reveal the recent invasion of the transposable element opus, absent in specimens from the 1800s and present from 1933 onward.
These case studies highlight the pipeline's ability to efficiently process large numbers of samples and facilitate longitudinal tracking of genomic features in diverse species.
Written by urgent.news from bioRxiv's reporting — not their text. Machine-written — may contain errors; check the original before relying on it.
