Pseudoassembly of k-mers
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.
02 /Specification & Classification
Click any tag to browse matching papers- Citations
- 2
- Organism
- Assay
- Research Focus
- Approach
Reproducibility ledger
Nobody has reported trying to reproduce this paper yet. Did you replicate an experiment or run the code? Your report saves the next lab a week.
Sign in to file a reproducibility report.
Related papers
- Mapping-free variant calling using haplotype reconstruction from k-mer frequencies
Peter A. Audano, Shashidhar Ravishankar, Fredrik O. Vannberg·BioinformaticsPeer-reviewed·Nov 23, 2017
- Reference-based variant detection with varseek
Joseph Matthew Rich, Laura Luebbert, … Lior S. Pachter·bioRxiv·Sep 3, 2025
- KmerKeys: a web resource for searching indexed genome assemblies and variants
Dmitri S. Pavlichin, HoJoon Lee, … Hanlee P. Ji·Nucleic Acids ResearchPeer-reviewed·Apr 21, 2022
- K2R: Tinted de Bruijn Graphs implementation for efficient read extraction from sequencing datasets
Léa Vandamme, Bastien Cazaux, Antoine Limasset·Bioinformatics AdvancesPeer-reviewed·Dec 26, 2024
- Integrating long-range connectivity information into de Bruijn graphs
Isaac Turner, Kiran V. Garimella, … Gil McVean·BioinformaticsPeer-reviewed·Mar 15, 2018
- Population-scale detection of non-reference sequence variants using colored de Bruijn Graphs
Thomas Krannich, W Timothy J White, … Birte Kehr·BioinformaticsPeer-reviewed·Oct 28, 2021