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PipeCraft: Flexible open-source toolkit for bioinformatics analysis of custom high-throughput amplicon sequencing
Sten Anslan1, Mohammad Bahram1,2, Indrek Hiiesalu1
1Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia.
Molecular Ecology Resources
|May 26, 2017
Summary
PipeCraft is a user-friendly bioinformatics pipeline for analyzing amplicon sequencing data. It offers customizable workflows for various platforms, enabling efficient data processing within 24 hours.
Area of Science:
- Environmental sciences
- Bioinformatics
- Genomics
Background:
- High-throughput sequencing generates vast data requiring multi-step analysis.
- Existing bioinformatics pipelines often lack flexibility for complex or customized designs.
Purpose of the Study:
- Introduce PipeCraft, a flexible bioinformatics pipeline with a graphical interface.
- Enable customization of amplicon sequencing data analysis workflows.
Main Methods:
- PipeCraft integrates multiple public bioinformatics tools.
- Provides a user-friendly graphical interface for tool selection and customization.
- Supports data from Illumina, Pacific Biosciences, Ion Torrent, and Roche 454 platforms.
Main Results:
- PipeCraft successfully processed large datasets from three sequencing platforms within 24 hours.
- The graphical user interface and automated tool linking facilitate workflow customization.
- All analytical steps are recorded in traceable log files.
Conclusions:
- PipeCraft offers a flexible and efficient solution for amplicon sequencing data analysis.
- Its user-friendly interface and customization options benefit researchers in environmental sciences and beyond.
