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martinfthomsen / rucs2

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Faster alignment algorithm #7

Open martinfthomsen opened 1 year ago

martinfthomsen commented 1 year ago
  1. The current alignment algorithm (BWA) for aligning the many kmers to the references is slow. Can a faster algorithm with just as good alignment performance be implemented?
  2. Even the creation of the fastq files to work with the BWA algorithm takes some time. Maybe this can be shaven down too by implementing another algorithm which can take a simpler input format?
  3. A third suggestion. For building the contigs/scaffolds, can the alignment to the references be done in one step, using a references which concatenates all the references into one super reference, or will this cause issues?