Genome assembly forensics: finding the elusive mis-assembly

Table 1 Accuracy of amosvalidate mis-assembly signatures and suspicious regions summarized for 16 bacterial genomes assembled with Phrap

Species name, genome length (Len), number of assembled contigs (Ctgs), and alignment inferred mis-assemblies (Errs) are given in the first four columns. Number of mis-assembly signatures output by amosvalidate (Num) is given in column 5, along with the number of signatures coinciding with a known mis-assembly in column 6 (Valid), and percentage of known mis-assemblies identified by one or more signatures in column 7 (Sens). The same values are given in columns 8-10 for the suspicious regions output by amosvalidate. The suspicious regions represent at least two different, coinciding lines of evidence, whereas the signatures represent a single line of evidence. A signature or region is deemed 'validated' if its location interval overlaps a mis-assembled region identified by dnadiff. Thus, a single signature or region can identify multiple mis-assemblies, and vice versa, a single mis-assembly can be identified by multiple signatures or regions.

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