Fig. 3

Graphical Depiction of Tager 104 Assembly. The Tager 104 genome was scaffolded using three separate technologies: contigs from MiSeq reactions (red tiling), PacBio RS reads (yellow histogram), and scaffolds produced from the hybrid assembly of both (blue tiling). However, assembly of the Tager 104 genome using these technologies were found insufficient alone, due to the presence of repeat regions. More specifically, long repeats (>500 bp) create errors in de Bruijn graph untangling (gray tiling). In addition, the exact placement of short repeats, such as interspersed nuclear elements (light blue tiling), RNA sequences (light red tiling) and simple repeats (light green tiling) create errors in construction. Areas rich in repeats and low in sequencing coverage (Regions 1 and 2) reveal difficulties in genomic construction. These difficulties were overcome by providing the construction algorithms with 20 kbp mate-pair information, provided by Lucigen NxSeq libraries