PALEOMIX

PALEOMIX automates processing and analysis of next-generation sequencing (NGS) data from ancient and modern genomes for paleogenomic, comparative genomic, and metagenomic investigations.

Key Features:

• Adapter removal: Cleans raw NGS reads by removing sequencing adapters to prepare data for downstream analyses.
• Read mapping: Aligns reads against reference genomes to enable comparative and variant analyses.
• PCR duplicate removal: Identifies and removes PCR-generated duplicate reads to reduce biases in downstream results.
• Postmortem damage characterization: Detects and accounts for postmortem DNA damage patterns typical of ancient DNA samples.
• Variant calling (SNP calling): Performs single nucleotide polymorphism (SNP) calling from mapped sequencing data.
• Phylogenomic inference: Applies maximum-likelihood methods for phylogenetic analysis.
• Metagenomic profiling: Profiles metagenomic content to characterize microbial communities in samples.
• Whole-genome resequencing workflows: Automates end-to-end processing steps commonly used in whole-genome resequencing studies.

Scientific Applications:

• Paleogenomics: Reconstruction and analysis of complete ancient genomes from NGS data while accounting for postmortem DNA damage.
• Comparative genomics: Comparison of ancient and modern genomes through mapping and SNP calling, exemplified by applications to Phytophthora infestans genomes.
• Metagenomics: Characterization of microbial communities present in ancient and modern specimens via metagenomic profiling.

Methodology:

Processes raw NGS reads through adapter removal, read mapping to reference genomes, PCR duplicate removal, postmortem DNA damage characterization, SNP calling, maximum-likelihood phylogenetic inference, and metagenomic profiling.