Quantifying and reducing spurious alignments for the analysis of ultra-short ancient DNA sequences.

ABSTRACT:

Background

The study of ancient DNA is hampered by degradation, resulting in short DNA fragments. Advances in laboratory methods have made it possible to retrieve short DNA fragments, thereby improving access to DNA preserved in highly degraded, ancient material. However, such material contains large amounts of microbial contamination in addition to DNA fragments from the ancient organism. The resulting mixture of sequences constitutes a challenge for computational analysis, since microbial sequences are hard to distinguish from the ancient sequences of interest, especially when they are short.

Results

Here, we develop a method to quantify spurious alignments based on the presence or absence of rare variants. We find that spurious alignments are enriched for mismatches and i

SUBMITTER: de Filippo C 

PROVIDER: S-EPMC6202837 | biostudies-literature | 2018 Oct

REPOSITORIES: biostudies-literature