PileLineGUI: a desktop environment for handling genome position files in next-generation sequencing studies.

PileLineGUI: a desktop environment for handling genome position files in next-generation sequencing studies.

Abstract

Next-generation sequencing (NGS) technologies are making sequence data available on an unprecedented scale. In this context, new catalogs of Single Nucleotide Polymorphism and mutations generated by resequencing studies are usually stored in genome position files (e.g. Variant Call Format, SAMTools pileup, BED, GFF) comprising of large lists of genomic positions, which are difficult to handle by researchers. Here, we present PileLineGUI, a novel desktop application primarily designed for manipulating, browsing and analysing genome position files (GPF), with specific support to somatic mutation finding studies. The developed tool also integrates a new genome browser module specially designed for inspecting GPFs. PileLineGUI is free, multiplatform and designed to be intuitively used by biomedical researchers. PileLineGUI is available at: http://sing.ei.uvigo.es/pileline/pilelinegui.html.

PileLine GUI is a front-end of the PileLine toolkit, plus a genome browser. With this intuitive graphical desktop application you can run the following tasks:

1. Processing commands of GP files, like seek, join, annotate and filtering.
2. Perform 2-samples and n-samples point somatic mutation calling (via the PileLine 2smc and nsmc commands).
3. Browse GP files in a interactive local genome browser.

You can download PileLine GUI from Downloads.

General scheme of the PileLine GUI software.

PileLine GUI's interactive genome browser.

PileLine GUI showing a instantly-navigable .pileup file.