PyDamage: automated ancient damage identification and estimation for contigs in ancient DNA de novo assembly.

ABSTRACT: DNA de novo assembly can be used to reconstruct longer stretches of DNA (contigs), including genes and even genomes, from short DNA sequencing reads. Applying this technique to metagenomic data derived from archaeological remains, such as paleofeces and dental calculus, we can investigate past microbiome functional diversity that may be absent or underrepresented in the modern microbiome gene catalogue. However, compared to modern samples, ancient samples are often burdened with environmental contamination, resulting in metagenomic datasets that represent mixtures of ancient and modern DNA. The ability to rapidly and reliably establish the authenticity and integrity of ancient samples is essential for ancient DNA studies, and the ability to distinguish between ancient and modern seq

SUBMITTER: Borry M 

PROVIDER: S-EPMC8323603 | biostudies-literature | 2021

REPOSITORIES: biostudies-literature