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Is there an open source project that tries to replicate the Seven Bridges proprietary graphing technology? It seems like a logical next step.

a_bonobo 10y ago
There are many people working on various aspects of DNA graphs - for example, there's now the FASTG format, a replacement for the FASTA format which is essentially a graph in text form: http://fastg.sourceforge.net/ http://fastg.sourceforge.net/ Some assemblers (SPAdes?) have started to support this format, but most downstream software only uses the FASTA format (the non-graph version from a single genome/representation). Heng Li (somewhat now the godfather of bioinformatics) wrote a blog post about various implementations here: https://lh3.github.io/2014/07/25/on-the-graphical-representation-of-sequences/ https://lh3.github.io/2014/07/25/on-the-graphical-representa...
- a_bonobo 10y ago
  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).
- roye 10y ago
  The more relevant continuation of Heng Li's posts is Pall Melsted et al's work on GFA: https://github.com/GFA-spec/GFA-spec https://github.com/GFA-spec/GFA-spec This is pretty close to my area...
roye 10y ago
The main one is vg, which I think Benedict Paten is actively supervising, along with Richard Durbin. The main developer is Erik Garrison. I'm pretty surprised it wasn't mentioned by name: https://github.com/vgteam/vg https://github.com/vgteam/vg

a_bonobo 10y ago

There are many people working on various aspects of DNA graphs - for example, there's now the FASTG format, a replacement for the FASTA format which is essentially a graph in text form: http://fastg.sourceforge.net/ http://fastg.sourceforge.net/ Some assemblers (SPAdes?) have started to support this format, but most downstream software only uses the FASTA format (the non-graph version from a single genome/representation). Heng Li (somewhat now the godfather of bioinformatics) wrote a blog post about various implementations here: https://lh3.github.io/2014/07/25/on-the-graphical-representation-of-sequences/ https://lh3.github.io/2014/07/25/on-the-graphical-representa...

a_bonobo 10y ago
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).
roye 10y ago
The more relevant continuation of Heng Li's posts is Pall Melsted et al's work on GFA: https://github.com/GFA-spec/GFA-spec https://github.com/GFA-spec/GFA-spec This is pretty close to my area...

roye 10y ago

The main one is vg, which I think Benedict Paten is actively supervising, along with Richard Durbin. The main developer is Erik Garrison. I'm pretty surprised it wasn't mentioned by name: https://github.com/vgteam/vg https://github.com/vgteam/vg