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P eak S tudio: a tool for the visualization and analysis of fragment analysis files
Author(s) -
McCafferty Jonathan,
Reid Robert,
Spencer Melanie,
Hamp Timothy,
Fodor Anthony
Publication year - 2012
Publication title -
environmental microbiology reports
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.229
H-Index - 69
ISSN - 1758-2229
DOI - 10.1111/j.1758-2229.2012.00368.x
Subject(s) - visualization , computer science , fragment (logic) , cluster analysis , java , principal component analysis , hierarchical clustering , suite , graphical user interface , studio , computational biology , operating system , data mining , biology , programming language , artificial intelligence , history , archaeology , telecommunications
Summary While emerging technologies such as next‐generation sequencing are increasingly important tools for the analysis of metagenomic communities, molecular fingerprinting techniques such as automated ribosomal intergenic spacer analysis ( ARISA ) and terminal restriction fragment length polymorphisms ( T‐RFLP ) remain in use due to their rapid speed and low cost. P eak S tudio is a java‐based graphical user interface ( GUI ) designed for the visualization and analysis of fragment analysis ( FSA ) files generated by the A pplied B iosystems capillary electrophoresis instrument. Specifically designed for ARISA and T‐ RFLP experiments, P eak S tudio provides the user the ability to freely adjust the parameters of a peak‐calling algorithm and immediately see the implications for downstream clustering by principal component analysis. P eak S tudio is fully open‐source and, unlike proprietary solutions, can be deployed on any computer running W indows, OS X or L inux. P eak S tudio allows data to be saved in multiple formats and can serve as a pre‐processing suite that prepares data for statistical analysis in programs such as SAS or R .