Introduction

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 under the GNU LGPL license. Full documentation including common use cases and guided analysis workflows is available at http://sing.ei.uvigo.es/pileline.

Publications

  1. PileLine: a toolbox to handle genome position information in next-generation sequencing studies.
    Cite this
    Glez-Peña D, Gómez-López G, Reboiro-Jato M, Fdez-Riverola F, Pisano DG, 2011-01-01 - BMC bioinformatics

Credits

  1. Daniel Glez-Peña
    Developer

  2. Gonzalo Gómez-López
    Developer

  3. Miguel Reboiro-Jato
    Developer

  4. Florentino Fdez-Riverola
    Developer

  5. David G Pisano
    Investigator

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Summary
AccessionBT000019
Tool TypeApplication
Category
PlatformsLinux/Unix
Technologies
User InterfaceTerminal Command Line
Download Count0
Submitted ByDavid G Pisano