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BMCBI
2011

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

9 years 5 months ago
PileLine: a toolbox to handle genome position information in next-generation sequencing studies
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.ne...
Daniel Glez-Peña, Gonzalo Gómez-L&oa
Added 12 May 2011
Updated 12 May 2011
Type Journal
Year 2011
Where BMCBI
Authors Daniel Glez-Peña, Gonzalo Gómez-López, Miguel Reboiro-Jato, Florentino Fdez-Riverola, David G. Pisano
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