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dc.contributor.authorBirkeland, Åsmund
dc.contributor.authorChyzynska, Katarzyna
dc.contributor.authorValen, Eivind
dc.PublishedBirkeland ÅR, Chyzynska K, Valen E. Shoelaces: An interactive tool for ribosome profiling processing and visualization. BMC Genomics. 2018;19:543eng
dc.description.abstractBackground: The emergence of ribosome profiling to map actively translating ribosomes has laid the foundation for a diverse range of studies on translational regulation. The data obtained with different variations of this assay is typically manually processed, which has created a need for tools that would streamline and standardize processing steps. Results: We present Shoelaces, a toolkit for ribosome profiling experiments automating read selection and filtering to obtain genuine translating footprints. Based on periodicity, favoring enrichment over the coding regions, it determines the read lengths corresponding to bona fide ribosome protected fragments. The specific codon under translation (P-site) is determined by automatic offset calculations resulting in sub-codon resolution. Shoelaces provides both a user-friendly graphical interface for interactive visualisation in a genome browser-like fashion and a command line interface for integration into automated pipelines. We process 79 libraries and show that studies typically discard excessive amounts of quality data in their manual analysis pipelines. Conclusions: Shoelaces streamlines ribosome profiling analysis offering automation of the processing, a range of interactive visualization features and export of the data into standard formats. Shoelaces stores all processing steps performed in an XML file that can be used by other groups to exactly reproduce the processing of a given study. We therefore anticipate that Shoelaces can aid researchers by automating what is typically performed manually and contribute to the overall reproducibility of studies. The tool is freely distributed as a Python package, with additional instructions, tutorial and demo datasets available at
dc.rightsAttribution CC BYeng
dc.subjectRibosome profilingeng
dc.titleShoelaces: An interactive tool for ribosome profiling processing and visualizationen_US
dc.typePeer reviewed
dc.typeJournal article
dc.rights.holderCopyright 2018 The Author(s)en_US
dc.source.journalBMC Genomics
dc.relation.projectBergens forskningsstiftelse: Valen
dc.relation.projectNorges forskningsråd: 250049

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