Open AccessPileLineGUI: a desktop environment for handling genome position files in next-generation sequencing studies
Author(s) -
Hugo López-Fernández,
Daniel Glez-Peña,
Miguel Reboiro-Jato,
Gonzalo GómezLópez,
David G. Pisano,
Florentino Fdez-Riverola
Publication year - 2011
Publication title -
nucleic acids research
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 9.008
H-Index - 537
eISSN - 1362-4954
pISSN - 0305-1048
DOI - 10.1093/nar/gkr439
Subject(s) - biology , genome , genome browser , context (archaeology) , dna sequencing , reference genome , computational biology , genomics , file format , genetics , computer science , database , gene , paleontology
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.