passionlab/elba

Parallel String Graph Construction, Transitive Reduction, and Contig Generation for De Novo Genome Assembly

elba's Issues

Todos and self-issue

1. ERR_THRESHOLD and MAX_NUM_READS should become LOWER_KMER_FREQ and UPPER_KMER_FREQ
2. In BELLA those are command line input, in diBELLA 2D we need them at compile time to define MPI buffer but it should be better to pass them as input to cmake to enable some flexibility.
3. Print String matrix in matrix market format optionally (can be an ifdef it's mostly for development).