BioMed Research International

Research Article

Linking De Novo Assembly Results with Long DNA Reads Using the dnaasm-link Application

Table 4

Tandem repeat reconstruction efficiency.
  Motif len. [bp] Num of repet. NGS unitigs dnaasm-link without gap fill. dnaasm-link without gap filling dnaasm-link with gap fill.
+ GapFiller + Sealer + GapCloser
E. coli 181 3.0 - - - - - -
181 2.3 - - - - - -
178 1.9 - - + - - +
226 2.0 - - - - - +
113 2.7 - - - - - +
226 1.9 - - - - - -
200 2.0 - - - - - +
S. cerevisiae 135 1.9 - - - - - -
135 1.9 - - - - - -
135 3.1 - - - - - -
135 3.1 - - - - - -
135 1.9 - - - - - -
192 2.2 - - - - - -
192 2.1 - - - - - -
84 3.0 - - - - - -
1998 2.0 - - - - - -
207 2.1 - - - - - +
81 3.3 - - - - - +
189 1.9 - - - - - +
72 5.3 - - - - - +
189 2.3 - - - - - +
The table presents all tandem repeats in the E. coli and S. cerevisiae reference genomes. In the presented table “+” signs mean the correct reproduction of the specified repetitive fragment and “-” signs mean the lack of correct reconstruction. The presented results indicate that the usage of long DNA reads by dnaasm-link tool allows reconstructing some of tandem repeats.