Handling 2-node cycles in Assemblies Graph. A 2-node cycle in AG witness a putative inversion along a single contig in M and S. If there actually is an inversion, then mate-pair reads are aligned with the wrong orientation in one of the two contigs. We can use this information to provide in output a correct sequence (the blue one in the picture).
Vicedomini et al. BMC Bioinformatics 2013 14(Suppl 7):S6 doi:10.1186/1471-2105-14-S7-S6