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PipeCraft: Flexible open-source toolkit for bioinformatics analysis of custom high-throughput amplicon sequencing data
Univ Tartu, Inst Ecol & Earth Sci, Tartu, Estonia..ORCID iD: 0000-0002-2299-454X
Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology. Univ Tartu, Inst Ecol & Earth Sci, Tartu, Estonia.
Univ Tartu, Inst Ecol & Earth Sci, Tartu, Estonia..
Univ Tartu, Nat Hist Museum, Tartu, Estonia..
2017 (English)In: Molecular Ecology Resources, ISSN 1755-098X, E-ISSN 1755-0998, Vol. 17, no 6, p. e234-e240Article in journal (Refereed) Published
Abstract [en]

High-throughput sequencing methods have become a routine analysis tool in environmental sciences as well as in public and private sector. These methods provide vast amount of data, which need to be analysed in several steps. Although the bioinformatics may be applied using several public tools, many analytical pipelines allow too few options for the optimal analysis for more complicated or customized designs. Here, we introduce PipeCraft, a flexible and handy bioinformatics pipeline with a user-friendly graphical interface that links several public tools for analysing amplicon sequencing data. Users are able to customize the pipeline by selecting the most suitable tools and options to process raw sequences from Illumina, Pacific Biosciences, Ion Torrent and Roche 454 sequencing platforms. We described the design and options of PipeCraft and evaluated its performance by analysing the data sets from three different sequencing platforms. We demonstrated that PipeCraft is able to process large data sets within 24hr. The graphical user interface and the automated links between various bioinformatics tools enable easy customization of the workflow. All analytical steps and options are recorded in log files and are easily traceable.

Place, publisher, year, edition, pages
2017. Vol. 17, no 6, p. e234-e240
Keywords [en]
high-throughput sequencing, metabarcoding, pipeline, sequencing data analysis, software
National Category
Biological Systematics
Identifiers
URN: urn:nbn:se:uu:diva-342909DOI: 10.1111/1755-0998.12692ISI: 000415921900020PubMedID: 28544559OAI: oai:DiVA.org:uu-342909DiVA, id: diva2:1185871
Available from: 2018-02-26 Created: 2018-02-26 Last updated: 2018-02-26Bibliographically approved

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Bahram, Mohammad

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