Just realised that most of the above is from 2014 - here are some recent works: A novel data structure to store the whole graph: https://almob.biomedcentral.co

Just realised that most of the above is from 2014 - here are some recent works: A novel data structure to store the whole graph: https://almob.biomedcentral.com/articles/10.1186/s13015-016-0083-7 https://almob.biomedcentral.com/articles/10.1186/s13015-016-... Software is here: https://www.uni-ulm.de/in/theo/research/seqana.html https://www.uni-ulm.de/in/theo/research/seqana.html This one maps the whole DNA space using markers: http://www.nature.com/articles/ncomms7914 http://www.nature.com/articles/ncomms7914 Here's a paper that looks at the total genetic space of several individuals, but with read mapping alone, no graphs: http://genomebiology.biomedcentral.com/articles/10.1186/s13059-015-0757-3 http://genomebiology.biomedcentral.com/articles/10.1186/s130... Most of this is based on open source or openly available software. A big company that's closed source is NRGene from Israel, I've read good things about their DeNovoMAGIC/PanMAGIC but I'm unsure how that stuff works exactly (apart from massive short read coverage).