title: 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.
authors.affiliation: Higher Technical School of Computer Engineering, University of Vigo, Ourense, Spain.
authors.forename: Hugo
authors.initials: H
authors.lastname: López-Fernández
authors.forename: Daniel
authors.initials: D
authors.lastname: Glez-Peña
authors.forename: Miguel
authors.initials: M
authors.lastname: Reboiro-Jato
authors.forename: Gonzalo
authors.initials: G
authors.lastname: Gómez-López
authors.forename: David G
authors.initials: DG
authors.lastname: Pisano
authors.forename: Florentino
authors.initials: F
authors.lastname: Fdez-Riverola
mesh_terms: D016678:Genome; D059014:High-Throughput Nucleotide Sequencing; D009154:Mutation; D020641:Polymorphism, Single Nucleotide; D017422:Sequence Analysis, DNA; D012984:Software