An open-sourced bioinformatic pipeline for the processing of Next-Generation Sequencing derived nucleotide reads: Identification and authentication of ancient metagenomic DNA

Abstract

Bioinformatic pipelines optimised for the processing and assessment of metagenomic ancient DNA (aDNA) are needed for studies that do not make use of high yielding DNA capture techniques. These bioinformatic pipelines are traditionally optimised for broad aDNA purposes, are contingent on selection biases and are associated with high costs. Here we present a bioinformatic pipeline optimised for the identification and assessment of ancient metagenomic DNA without the use of expensive DNA capture techniques. Our pipeline actively conserves aDNA reads, allowing the application of a bioinformatic approach by identifying the shortest reads possible for analysis (22-28bp). The time required for processing is drastically reduced through the use of a 10% segmented non-redundant sequence file (229 hours to 53). Processing speed is improved through the optimisation of BLAST parameters (53 hours to 48). Additionally, the use of multi-alignment authentication in the identification of taxa increases overall confidence of metagenomic results. DNA yields are further increased through the use of an optimal MAPQ setting (MAPQ 25) and the optimisation of the duplicate removal process using multiple sequence identifiers (a 4.35-6.88% better retention). Moreover, characteristic aDNA damage patterns are used to bioinformatically assess ancient vs. modern DNA origin throughout pipeline development. Of additional value, this pipeline uses open-source technologies, which increases its accessibility to the scientific community.