CANGS DB: a stand-alone web-based database tool for processing, managing and analyzing 454 data in biodiversity studies

Ram Vinay Pandey,Jens Boenigk,Viola Nolte,Christian Schlötterer

doi:10.1186/1756-0500-4-227

Ram Vinay Pandey, Jens Boenigk + Show 2 more

Open Access

https://doi.org/10.1186/1756-0500-4-227

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Abstract

BackgroundNext generation sequencing (NGS) is widely used in metagenomic and transcriptomic analyses in biodiversity. The ease of data generation provided by NGS platforms has allowed researchers to perform these analyses on their particular study systems. In particular the 454 platform has become the preferred choice for PCR amplicon based biodiversity surveys because it generates the longest sequence reads. Nevertheless, the handling and organization of massive amounts of sequencing data poses a major problem for the research community, particularly when multiple researchers are involved in data acquisition and analysis. An integrated and user-friendly tool, which performs quality control, read trimming, PCR primer removal, and data organization is desperately needed, therefore, to make data interpretation fast and manageable.FindingsWe developed CANGS DB (Cleaning and Analyzing Next Generation Sequences DataBase) a flexible, stand alone and user-friendly integrated database tool. CANGS DB is specifically designed to organize and manage the massive amount of sequencing data arising from various NGS projects. CANGS DB also provides an intuitive user interface for sequence trimming and quality control, taxonomy analysis and rarefaction analysis. Our database tool can be easily adapted to handle multiple sequencing projects in parallel with different sample information, amplicon sizes, primer sequences, and quality thresholds, which makes this software especially useful for non-bioinformaticians. Furthermore, CANGS DB is especially suited for projects where multiple users need to access the data. CANGS DB is available at http://code.google.com/p/cangsdb/.ConclusionCANGS DB provides a simple and user-friendly solution to process, store and analyze 454 sequencing data. Being a local database that is accessible through a user-friendly interface, CANGS DB provides the perfect tool for collaborative amplicon based biodiversity surveys without requiring prior bioinformatics skills.

Highlights

Generation sequencing (NGS) is widely used in metagenomic and transcriptomic analyses in biodiversity
Being a local database that is accessible through a user-friendly interface, CANGS DB provides the perfect tool for collaborative amplicon based biodiversity surveys without requiring prior bioinformatics skills
We developed CANGS DB as an integrated user-friendly database tool that can be installed on local computers and accessed through the internet by standard browsers

Summary

Introduction

Generation sequencing (NGS) is widely used in metagenomic and transcriptomic analyses in biodiversity. The ease of data generation provided by NGS platforms has allowed researchers to perform these analyses on their particular study systems. In particular the 454 platform has become the preferred choice for PCR amplicon based biodiversity surveys because it generates the longest sequence reads. An integrated and user-friendly tool, which performs quality control, read trimming, PCR primer removal, and data organization is desperately needed, to make data interpretation fast and manageable. An effective data analysis requires the ability to link additional data, such as time of collection and ecological variables, to the sequences. Researchers need an analytical tool that provides the flexibility to handle different PCR primers

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