Journal
BIOINFORMATICS
Volume 27, Issue 15, Pages 2153-2155Publisher
OXFORD UNIV PRESS
DOI: 10.1093/bioinformatics/btr347
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Funding
- Danish Council for Independent Research
- Natural Sciences (FNU)
- Danish National Research Foundation (Danmarks Grundforskningsfond)
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Ancient DNA extracts consist of a mixture of contaminant DNA molecules, most often originating from environmental microbes, and endogenous fragments exhibiting substantial levels of DNA damage. The latter introduce specific nucleotide misincorporations and DNA fragmentation signatures in sequencing reads that could be advantageously used to argue for sequence validity. mapDamage is a Perl script that computes nucleotide misincorporation and fragmentation patterns using next-generation sequencing reads mapped against a reference genome. The Perl script outputs are further automatically processed in embedded R script in order to detect typical patterns of genuine ancient DNA sequences.
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