Include circles when creating unitigs in the graph maker

bioinfologics / sdg

Sequence Distance Graph framework: graph + reads + mapping + analysis

MIT License

25 stars 6 forks source link

Include circles when creating unitigs in the graph maker #101

Closed TransGirlCodes closed 5 years ago

TransGirlCodes commented 5 years ago

Cases where a canonical kmer has a canonical neighbour that is itself, will get dropped from the graph currently with the new dbg building algorithm. E.g ATA has a fw AND bw neighbour TAT (canonically ATA), and so the unitig ATAT would be dropped from the graph. This is an example of the more general circle problem: at the end of the unitig creation, any kmers that are not used will be in circles: We can add those circles as unitigs by choosing a random break point.

bjclavijo commented 5 years ago

when the circles are simplest (i.e ATATATATA.... etc) a single kmer is created but it is not connected

bjclavijo commented 5 years ago

solved on 4b64d1cf456c1c897a624a0c03c9f86248a605b1