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ESTPiper--a web-based analysis pipeline for expressed sequence tags.

Zuojian Tang¹, Jeong-Hyeon Choi, Chris Hemmerich

¹The Center for Genomics and Bioinformatics, Indiana University, Bloomington, Indiana, USA. tangz@cgb.indiana.edu

|April 23, 2009

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ESTPiper is a web-based pipeline simplifying large-scale Expressed Sequence Tag (EST) data analysis. It offers modular components for base calling, assembly, and annotation, enhancing research reproducibility and accessibility for biologists.

Area of Science:

Bioinformatics
Computational Biology
Genomics

Background:

Express Sequence Tag (EST) sequencing is increasingly accessible to individual labs.
Processing large EST datasets presents a significant challenge for researchers.
Web-based tools are crucial for efficient EST data analysis in the biological community.

Purpose of the Study:

To develop a user-friendly, web-based pipeline for streamlining large-scale EST analysis.
To provide a comprehensive solution for various EST processing tasks.
To support the growing needs of the research community for accessible bioinformatics tools.

Main Methods:

Developed ESTPiper, a modular web-based analysis pipeline.
Integrated components for base calling, data cleaning, assembly, and genome alignment.

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Enabled user control over parameters and batch processing for flexibility.

Main Results:

ESTPiper offers an intuitive interface for EST analysis, including annotation and gene ontology analysis.
Modular design allows for separate or combined execution of analysis steps.
Provides extensive documentation, downloadable intermediate results, and reproducible run histories.

Conclusions:

ESTPiper effectively streamlines the complex process of EST data analysis.
A publicly accessible web server and freely available software support diverse project sizes.
Facilitates EST analysis for projects ranging from small-scale to large initiatives like the Daphnia pulex project.