Name
Title | ||
|---|---|---|
Mapping-Free and Assembly-Free Discovery of Inversion Breakpoints from Raw NGS Reads. |
Abstract | ||
|---|---|---|
We propose a formal model and an algorithm for detecting inversion breakpoints without a reference genome, directly from raw NGS data. This model is characterized by a fixed size topological pattern in the de Bruijn Graph. We describe precisely the possible sources of false positives and false negatives and we additionally propose a sequence-based filter giving a good trade-off between precision and recall of the method. We implemented these ideas in a prototype called TakeABreak. Applied on simulated inversions in genomes of various complexity (from E. coli to a human chromosome dataset), TakeABreak provided promising results with a low memory footprint and a small computational time. |
Year | DOI | Venue |
|---|---|---|
2014 | 10.1007/978-3-319-07953-0_10 | ALGORITHMS FOR COMPUTATIONAL BIOLOGY |
Keywords | Field | DocType |
structural variant,NGS,reference-free,de Bruijn graph | Genome,Inversion (meteorology),Computer science,Precision and recall,Algorithm,De Bruijn graph,Breakpoint,False positives and false negatives,Memory footprint,Reference genome | Conference |
Volume | ISSN | Citations |
8542 | 0302-9743 | 4 |
PageRank | References | Authors |
0.46 | 6 | 3 |
Name | Order | Citations | PageRank |
|---|---|---|---|
| Claire Lemaitre | 1 | 66 | 5.87 |
| Liviu Ciortuz | 2 | 24 | 4.84 |
| Pierre Peterlongo | 3 | 390 | 20.28 |