Fig. 1

Flowchart describing the whole pipeline from genome assembly to finishing that includes the generation of input data for WiseScaffolder (top), the semi-automatic scaffolder itself (middle) and the manual scaffolding and genome finishing steps (bottom). Dark grey boxes correspond to raw sequencing data, light blue boxes to either input files for WiseScaffolder or to exchange files used during the scaffolding process, the dark blue box to the outputs of WiseScaffolder and light grey boxes to the different genome stages along the whole pipeline. The four capital letters correspond to the four subcommands of WiseScaffolders