Fig. 9

AliTV plot [48] showing alignments of the different assemblers compared to each other and the reference. Each blue bar in the plot corresponds to an assembly of the Oryza brachyantha chloroplast (DRR053294). Regions in adjacent assemblies are connected with colored ribbons for similar regions in the alignment with identity coded as color from red to green. The purple arrows on the assemblies depict the IR regions. This plot highlights some common problems with chloroplast assembly. Chloroplast assembly protocol only assembled small fragments mostly from the IR region. IOGA returned three separate contigs corresponding to LSC, SSC, and IR. Fast-Plast and GetOrganelle produced assemblies that were identical to the reference. chloroExtractor has the same structure but the LSC is flipped compared to the reference (which is a biologically valid option). Both NOVOPlasty and ORG.Asm had the SSC flipped compared to the reference and did not start with the LSC but the IR and SSC, respectively (the start point is arbitrary in a circular sequence)