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The consensus between these reads is clear, but I'm having trouble assembling the entire contig. There are a few sequencing errors (especially in the T-rich region following the 13-read exact consensus) that are truncating the assembly. Linear path assembly isn't designed to handle this case, but the junction count assembler is producing very small contigs as well.
My thought was to try the SimpleLabeledAssembler to label across high-degree nodes, but this requires passing in a sequence when finding high-degree nodes and labeling. What should this sequence be? In the general case I won't have the consensus sequence beforehand: this is what I'm trying to assemble. :)
The text was updated successfully, but these errors were encountered:
I have 13 reads that form the following graph structure at k=31 (reads here).
With some pretty vanilla parameters, the 13 reads align very well and have nearly perfect consensus.
The consensus between these reads is clear, but I'm having trouble assembling the entire contig. There are a few sequencing errors (especially in the T-rich region following the 13-read exact consensus) that are truncating the assembly. Linear path assembly isn't designed to handle this case, but the junction count assembler is producing very small contigs as well.
My thought was to try the SimpleLabeledAssembler to label across high-degree nodes, but this requires passing in a sequence when finding high-degree nodes and labeling. What should this sequence be? In the general case I won't have the consensus sequence beforehand: this is what I'm trying to assemble. :)
The text was updated successfully, but these errors were encountered: