Fig. 2

Overview of differences between scaffolds and reference according to BLASTN alignments. Solid lines indicate reference (top) and scaffolds (bottom) respectively, red lines indicate unaligned segments, dashed lines between reference and scaffolds indicate alignment borders. a Scaffold is perfectly aligned to the genome reference. b Insertion or deletion error in scaffolds. An insertion/deletion error in scaffold causes alignment breaks, and the scaffold will be split into several aligned segments separated by the insertion/deletion error. c Misjoin in scaffold. Assembly errors caused by joining distinct genome regions with large distance (top left), by joining segments which can be aligned to different reference strands (top right), or by joining segments between different chromosomes (in eukaryotes) or between chromosome and plasmid (in bacteria) (bottom left). The yellow solid line indicates the region of reverse strand of the reference region. d Scaffolds that have entirely no alignment information (left) or have partial unaligned segments relative to the scaffold (right). We treat these situations as insertions that may be caused by assembly errors or by novel sequences in target genome