Pseudoassembly of k-mers.

We introduce a approach to identifying variation in sets of genomic sequences via colored de Bruijn graphs. Our pseudoassembly method is implemented in a program called klue that assembles k-mers into sequences compatible with a variant-aware extension of pseudoalignment. We show that this approach can be used to identify cell-type specific variants from single-cell RNA-seq in a mouse melanoma model.