Fig. 1

The ClusTrast pipeline. Orange ovals denote input data, black squares denote actions taken by ClusTrast, blue arrows denote intermediate data file transfers, yellow oval denotes output final assembly, and the black rhomboid and oval handle the guiding contig user input status. The only required input to ClusTrast is a short read RNA-seq data set (orange oval in top left corner). Guiding contigs may optionally be input by the user (dashed orange oval in top right corner, and green arrows followed if provided. They may also be used as primary assembly (not depicted)). If guiding contigs are not provided by the user, the primary assembly is repurposed and used also as guiding contigs (red arrows). SR = short reads, GCs = guiding contigs