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GAM-LRS: genomic assemblies merger including long read sequencing data

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Manthey, G. (2020). GAM-LRS: genomic assemblies merger including long read sequencing data. Bachelor Thesis, Kiel University, Kiel.


Cite as: http://hdl.handle.net/21.11116/0000-0007-A7CC-7
Abstract
Most genetic studies rely on the completeness and correctness of a reference genome.Even though modern sequencing techniques offer ever more improved genome assem-blies, the results are not complete and error free assemblies can not be guaranteed.With new sequencing techniques, many scientists have updated the reference genome oftheir study species. Although these newer references are more continuous and have lesserrors than the existing reference, the new reference could be improved by integratingthe already existing data from the former reference. To accomplish such a merging weimplemented the Genomic Assemblies Merger including Long Read Sequencing data(GAM-LRS). We chose the assembly reconciliation program GAM-NGS as a basis todevelop GAM-LRS.GAM-LRS accomplishes the merging of two reference genomes of the bird speciesSylvia atricapilla, where traditional assembly reconciliation programs failed. On thetask of assembly reconciliation GAM-LRS performs similar to assembly reconciliationprograms on GAGE datasets. There are still some major errors in GAM-LRS whichhave to be fixed before the program is made public. However, the goal for the futureof GAM-LRS is to make it publicly available for all scientists with multiple referencegenomes available.