Speaker
Description
High-throughput sequencing is now central to biodiversity assessment and paleoecological reconstruction, both relying on multi-step pipelines whose choices shape ecological interpretation. Existing solutions are either flexible but poorly documented scripts, or standardized but rigid, infrastructure-heavy platforms, leaving little room for adaptable tools. We address this gap with two complementary, Snakemake-based workflows for different sequencing strategies.
AMPBA (Accessible Metabarcoding Platform for Biodiversity Analysis; https://helmholtz.software/software/ampba-workflow) addresses amplicon metabarcoding for biodiversity assessment and monitoring. Because markers differ in taxa, evolutionary rate, and resolution, AMPBA decouples feature generation from any fixed biodiversity unit: denoising, clustering, and cooccurrence collapse each build a new unit (ASVs, swarm/OTU clusters, cASVs/cOTUs) from whichever precedes it, while NUMT filtering, decontamination, and replicate merging refine rather than redefine it; taxonomic assignment switches independently between marker-specific classifier/database pairs.
sedaECHO (https://gitlab.awi.de/data-science-team/sedaecho) addresses shotgun metagenomic analysis of sedimentary ancient DNA (sedaDNA), enabling high-resolution reconstruction of past ecosystems by capturing taxa that rarely appear in the fossil record. It ensures reproducibility through explicit rule definitions, pinned software versions, and traceable provenance, integrating established tools for taxonomic and functional classification and damage pattern authentication, and allowing multiple methods to run side by side under identical conditions.
Both pipelines share the same design philosophy: locally installable, workflow-managed, and modular, reducing setup complexity and enabling systematic comparison of methods. Together, they support standardized, reproducible analysis of environmental and ancient DNA across ecological and paleoecological research.