Automatic Outlier Detection for Genome Assembly Quality Assessment

Abstract

In this work we describe a method to automatically detect errors in de novo assembled genomes. The method extends a Bayesian assembly quality evaluation framework, ALE, which computes the likelihood of an assembly given a set of unassembled data. Starting from ALE output, this method applies outlier detection algorithms to identify the precise locations of assembly errors. We show results from a microbial genome with manually curated assembly errors. Our method detects all deletions, 82.3% of insertions, and 88.8% of single base substitutions. It was also able to detect an inversion error that spans more than 400 bases.