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. 2016 Aug 31;17 Suppl 5(Suppl 5):496.
doi: 10.1186/s12864-016-2824-x.

SPAI: an interactive platform for indel analysis

Mohammad Shabbir Hasan  1 , Liqing Zhang  2
Affiliations

SPAI: an interactive platform for indel analysis

Mohammad Shabbir Hasan et al. BMC Genomics. .

Abstract

Background: Insertions and Deletions (Indels) are the most common form of structural variation in human genome. Indels not only contribute to genetic diversity but also cause diseases. Therefore assessing indels in human genome has become an interesting topic to the research community. This increasing interest on indel calling research has resulted into the development of a good number of indel calling tools. However, all of these tools are command line based and require expertise from Computer Science (CS) to execute them which makes it challenging for researchers from non-CS background.

Methods: In this paper, we describe an interactive platform named SPAI which stands for Single Platform for Analyzing Indels.

Results: Being a Graphical User Interface (GUI) tool, SPAI facilitates users to run several popular indel calling tools and perform several analyses on the indel calling results without knowing any command line programming.

Conclusions: SPAI is written in Java and tested in Linux operating system.

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Figures

Fig. 1
Fig. 1
Main window of SPAI
Fig. 2
Fig. 2
Downloader window of SPAI
Fig. 3
Fig. 3
Comparing the results of different tools with benchmark dataset
Fig. 4
Fig. 4
Tabular display of a BAM file
See this image and copyright information in PMC

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