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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 pos- itives 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. Ap- plied 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.
Cited literature [12 references]
https://hal.inria.fr/hal-01063157
Contributor : Pierre Peterlongo Connect in order to contact the contributor
Submitted on : Monday, November 17, 2014 - 9:05:56 AM
Last modification on : Monday, November 22, 2021 - 1:52:23 PM
Long-term archiving on: : Wednesday, February 18, 2015 - 10:41:55 AM
Contributor : Pierre Peterlongo Connect in order to contact the contributor
Submitted on : Monday, November 17, 2014 - 9:05:56 AM
Last modification on : Monday, November 22, 2021 - 1:52:23 PM
Long-term archiving on: : Wednesday, February 18, 2015 - 10:41:55 AM
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Lemaitre2014_preprint.pdf
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