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

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 perf

SUBMITTER: Glez-Pena D 

PROVIDER: S-EPMC3037855 | biostudies-literature | 2011 Jan

REPOSITORIES: biostudies-literature