Open Access Highly Accessed Software

PileLine: a toolbox to handle genome position information in next-generation sequencing studies

Daniel Glez-Peña1*, Gonzalo Gómez-López2, Miguel Reboiro-Jato1, Florentino Fdez-Riverola1 and David G Pisano2

Author Affiliations

1 Higher Technical School of Computer Engineering, University of Vigo, Ourense, Spain

2 Bioinformatics Unit (UBio), Structural Biology and Biocomputing Programme, Spanish National Cancer Research Centre (CNIO), Madrid, Spain

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BMC Bioinformatics 2011, 12:31  doi:10.1186/1471-2105-12-31

Published: 24 January 2011

Abstract

Background

Genomic position (GP) files currently used in next-generation sequencing (NGS) studies are always difficult to manipulate due to their huge size and the lack of appropriate tools to properly manage them. The structure of these flat files is based on representing one line per position that has been covered by at least one aligned read, imposing significant restrictions from a computational performance perspective.

Results

PileLine implements a flexible command-line toolkit providing specific support to the management, filtering, comparison and annotation of GP files produced by NGS experiments. PileLine tools are coded in Java and run on both UNIX (Linux, Mac OS) and Windows platforms. The set of tools comprising PileLine are designed to be memory efficient by performing fast seek on-disk operations over sorted GP files.

Conclusions

Our novel toolbox has been extensively tested taking into consideration performance issues. It is publicly available at http://sourceforge.net/projects/pilelinetools webcite under the GNU LGPL license. Full documentation including common use cases and guided analysis workflows is available at http://sing.ei.uvigo.es/pileline webcite.