Fig. 5

Overview of the MetaCarvel pipeline: First, reads are aligned to assembled contigs. Using these alignments, a scaffold graph is constructed by bundling the link implying same contig orientation. In this graph, repeats are identified and removed. In the repeat removed scaffold graph, first variants are detected, and variant-aware contig layout is performed to generate final scaffolds. The output of the MetaCarvel pipeline is the sequences for scaffolds and the list of variants found in the scaffold graph