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Section: New Results

Genome scaffolding with contaminated data

Scaffolding is a cornerstone in the assembly of genomes from next-generation sequencing data. It consists in ordering assembled sequences according to their putative order and orientation in the source genome. However, we are almost always in a setting where the genome is not known. Instead, order and orientation of sequences are inferred from partial information present in the sequencing data.

Unfortunately, sequencing data is noisy and often has contamination, i.e. a subset of the data which indicates a wrong genome order and/or orientation. We have investigated this effect and designed the first algorithm that explicitly models this contamination to better perform scaffolding.

This work appeared in the proceedings of the WABI 2015 conference [9] and has been accepted to the Bioinformatics journal, currently under revision. This work is in collaboration with K. Sahlin and L. Arvestad (KTH, Sweden).