PASSion 1.2.1

:: DESCRIPTION

PASSion uses the mapped read in a pair as anchor and then uses a high resolution algorithm, pattern growth, to remap the proximal and distal fragments of the unmapped read to a local region of the reference indicated by the mate. It is capable of identifying both known and novel canonical and non-canonical junctions with SNP or sequencing error tolerance.

::DEVELOPER

Yanju Zhang (Leiden University Medical Center, The Netherlands): y.zhang AT lumc.nl

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux

Perl

SAMtools

:: DOWNLOAD

:: MORE INFORMATION

Citation:

PileLine 1.2 / PileLineGUI 1.3

:: DESCRIPTION

PileLine is a flexible command-line toolkit for efficient handling, filtering, and comparison of genomic position (GP) files produced by next-generation sequencing experiments (i.e. pileup, BED,GFF, or VCF files). PileLine is designed to be memory efficient by performing on-disk operations over sorted GP files directly.

PileLine GUI is a front-end of the PileLine toolkit, plus a genome browser.

::DEVELOPER

SING Group.

:: SCREENSHOTS

:: REQUIREMENTS

Linux / Windows / MacOsX
Java
Apache Ant

:: DOWNLOAD

PileLine / PileLineGUI

:: MORE INFORMATION

Citation

PileLine: a toolbox to handle genome position information in next-generation sequencing studies.
Glez-Peña D, Gómez-López G, Reboiro-Jato M, Fdez-Riverola F, Pisano DG.
BMC Bioinformatics. 2011 Jan 24;12:31.

PileLineGUI: a desktop environment for handling genome position files in next-generation sequencing studies.
López-Fernández H, Glez-Peña D, Reboiro-Jato M, Gómez-López G, Pisano DG, Fdez-Riverola F.
Nucleic Acids Res. 2011 Jul;39(Web Server issue):W562-6. Epub 2011 Jun 6.

Tag: PileLine

PASSion 1.2.1 – Pattern Growth algorithm based Pileline for Splice Site Detection in Paired-end RNA-Seq data

PASSion 1.2.1

PileLine 1.2 / PileLineGUI 1.3 – Handle Genome Position information in Next-generation Sequencing Studies

PileLine 1.2 / PileLineGUI 1.3