Jabba: Hybrid Error Correction for Long Sequencing Reads Using Maximal Exact Matches

Third generation sequencing platforms produce longer reads with higher error rates than second generation sequencing technologies. While the improved read length can provide useful information for downstream analysis, underlying algorithms are challenged by the high error rate. Error correction methods in which accurate short reads are used to correct noisy long reads appear to be attractive to generate high-quality long reads. Methods that align short reads to long reads do not optimally use the information contained in the second generation data, and suffer from large runtimes.

Frequency-based haplotype reconstruction from deep sequencing data of bacterial populations

Clonal populations accumulate mutations over time, resulting in different haplotypes. Deep sequencing of such a population in principle provides information to reconstruct these haplotypes and the frequency at which the haplotypes occur. However, this reconstruction is technically not trivial, especially not in clonal systems with a relatively low mutation frequency. The low number of segregating sites in those systems adds ambiguity to the haplotype phasing and thus obviates the reconstruction of genome-wide haplotypes based on sequence overlap information.

Dec/10 09:00
EDINBURGH GENOMICS The University of Edinburgh Ashworth Laboratories The King's Buildings Charlotte Auerbach Road Edinburgh EH9 3FL Scotland, United Kingdom

workshop "Oxford Nanopore MinION Sequencing - Data Handling, Analysis and Applications

Edinburgh Genomics is happy to offer a 1-day workshop "Oxford Nanopore MinION Sequencing - Data Handling, Analysis and Applications".


Nanopore sequencing is one of the newest sequence technologies, in which single DNA molecules are sequenced directly, without the need for an intervening PCR amplification step or a chemical labelling step. It offers the potential of read lengths of tens of kilo bases.


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