quicksand

quicksand combines fast alignment-free classification with post-classification mapping, filtering, and ancient DNA authentication for rapid taxonomic classification of mammalian mitochondrial DNA (mtDNA) in sedaDNA samples.

Key Features:

• Alignment-free classification: Uses KrakenUniq for fast taxonomic classification of sequences.
• Post-classification mapping: Performs mapping after initial classification to improve accuracy.
• Filtering: Applies filtering steps to reduce false positives from alignment-free methods.
• Ancient DNA authentication: Includes authentication steps specific to ancient DNA analysis.
• Nextflow pipeline: Implements the workflow as an open-source Nextflow pipeline for reproducible execution.

Scientific Applications:

• sedaDNA analysis: Enables taxonomic classification of mammalian mitochondrial DNA from sedimentary ancient DNA samples.
• Large-scale screening: Supports processing of large numbers of sedaDNA sequences for archaeological research.
• Past ecosystem reconstruction: Provides fine-grained information about composition of past ecosystems in the absence of skeletal remains.
• Human site use analysis: Informs about human site use through genetic analysis of archaeological sediments.

Methodology:

quicksand uses KrakenUniq for alignment-free classification, followed by post-classification mapping, filtering, and ancient DNA authentication. The pipeline was validated using simulations and reanalyses of published datasets.