Jun 29, 2018

Novo&Stitch: accurate reconciliation of genome assemblies via optical maps

Bioinformatics
Weihua PanStefano Lonardi

Abstract

De novo genome assembly is a challenging computational problem due to the high repetitive content of eukaryotic genomes and the imperfections of sequencing technologies (i.e. sequencing errors, uneven sequencing coverage and chimeric reads). Several assembly tools are currently available, each of which has strengths and weaknesses in dealing with the trade-off between maximizing contiguity and minimizing assembly errors (e.g. mis-joins). To obtain the best possible assembly, it is common practice to generate multiple assemblies from several assemblers and/or parameter settings and try to identify the highest quality assembly. Unfortunately, often there is no assembly that both maximizes contiguity and minimizes assembly errors, so one has to compromise one for the other. The concept of assembly reconciliation has been proposed as a way to obtain a higher quality assembly by merging or reconciling all the available assemblies. While several reconciliation methods have been introduced in the literature, we have shown in one of our recent papers that none of them can consistently produce assemblies that are better than the assemblies provided in input. Here we introduce Novo&Stitch, a novel method that takes advantage of optical m...Continue Reading

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Mentioned in this Paper

Genome
Novo Nordisk
Chimera Organism
Genome Assembly Sequence
Nucleic Acid Sequencing
Genome Mapping
Sequencing
Medication Reconciliation
Literature
Mullerian duct inhibiting substance

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