Blocks construction and coverage filtering. Blocks are identified by regions belonging to M and S that share a relatively high amount of mapped reads. In this figure, blue reads identify clusters of adjacent reads that are uniquely mapped in the same contig of both the assemblies. Moreover, GAM-NGS discards blocks like B3 that contains a small amount of shared reads compared to the number of reads aligned in the same regions (e.g., in B3 these are less than 35% and this block may create a wrong link between contigs).
Vicedomini et al. BMC Bioinformatics 2013 14(Suppl 7):S6 doi:10.1186/1471-2105-14-S7-S6