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Updated: Sep 19, 2025

Hybrid De Novo Genome Assembly for the Generation of Complete Genomes of Urinary Bacteria using Short- and Long-read Sequencing Technologies
Published on: August 20, 2021
Pseudoassembly of k-mers
Delaney K Sullivan1,2, Mayuko Boffelli3, Lior Pachter1,4
1Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA.
Abstract:
We introduce a pseudoassembly 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 de novo variants from single-cell RNA-seq in a mouse melanoma model.
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