DELLY 0.8.7 – integrated Split-read and Paired-end based Structural Variant Discovery in Deep sequencing data

DELLY 0.8.7

:: DESCRIPTION

DELLY is an integrated structural variant prediction method that can detect deletions, tandem duplications, inversions and translocations at single-nucleotide resolution in short-read massively parallel sequencing data. It uses paired-ends and split-reads to sensitively and accurately delineate genomic rearrangements throughout the genome.

::DEVELOPER

Korbel Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux

:: DOWNLOAD

DELLY

:: MORE INFORMATION

Citation

DELLY: structural variant discovery by integrated paired-end and split-read analysis
Tobias Rausch; Thomas Zichner; Andreas Schlattl; Adrian M. Stütz; Vladimir Benes; Jan O. Korbel
Bioinformatics 2012 28: i333-i339

PREGO 1.2 -Paired-End Reconstruction of Genome Organization

PREGO 1.2

:: DESCRIPTION

PREGO reconstructs a cancer genome as a rearrangement of segments, or intervals, from the reference genome using paired end sequencing data

::DEVELOPER

Raphael Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux/MacOsx/WIndows
Java

:: DOWNLOAD

PREGO

:: MORE INFORMATION

Citation:

L. Oesper, A. Ritz, S.J. Aerni, R. Drebin, and B.J. Raphael. (2012)
Reconstructing Cancer Genome Organization.
BMC Bioinformatics. 2012; 13(Suppl 6): S10.

3PEAT – Paired-End Analysis of Transcription Start Sites in Arabidopsis Reveals Plant-Specific Promoter Signatures

3PEAT

:: DESCRIPTION

3PEAT (Plant PEAT Peaks) predicts the probability of a TSS at any given nucleotide in the Arabidopsis genome solely from the DNA sequence surrounding that nucleotide.

::DEVELOPER

Megraw Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux

:: DOWNLOAD

3PEAT

:: MORE INFORMATION

Citation

Morton T, Petricka J, Corcoran DL, Li S, Winter CM, Carda A, Benfey PN, Ohler U, Megraw M. (2014).
Paired-end analysis of transcription start sites in Arabidopsis reveals plant-specific promoter signatures.
Plant Cell, 26:2746-60.

FusionSeq 0.7.0 – Detect Chimeric Transcripts from Paired-end RNA-seq Experiments

FusionSeq 0.7.0

:: DESCRIPTION

FusionSeq is a computational framework for detecting chimeric transcripts from paired-end RNA-seq experiments. It includes filters to remove spurious candidate fusions with artifacts, such as misalignment or random pairing of transcript fragments, and provides a ranked list of fusion-transcript candidates that can be further evaluated via experimental methods. FusionSeq also contains a module to identify exact sequences at breakpoint junctions.

::DEVELOPER

Gerstein Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux

:: DOWNLOAD

FusionSeq

:: MORE INFORMATION

Citation:

Andrea Sboner, Lukas Habegger, Dorothee Pflueger, Stephane Terry, David Z. Chen, Joel S. Rozowsky, Ashutosh K. Tewari, Naoki Kitabayashi, Benjamin J. Moss, Mark S. Chee, Francesca Demichelis, Mark A. Rubin, Mark B. Gerstein
FusionSeq: a modular framework for finding gene fusions by analyzing Paired-End RNA-Sequencing data
Genome Biology 21 Oct. 2010; 11:R104

EBARDenovo 2.0.1 – Highly-accurate de novo Assembler of Paired-end RNA-Seq

EBARDenovo 2.0.1

:: DESCRIPTION

EBARDenovo is a highly-accurate search-based de novo assembler of paired-end RNA-Seq for advance transcriptomic study.

::DEVELOPER

Frank Hsueh-Ting Chu

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Windows/ Linux/ MacOsX

:: DOWNLOAD

EBARDenovo

:: MORE INFORMATION

Citation

Bioinformatics. 2013 Apr 15;29(8):1004-1010. Epub 2013 Mar 1.
EBARDenovo: highly accurate de novo assembly of RNA-Seq with efficient chimera-detection.
Chu HT, Hsiao WW, Chen JC, Yeh TJ, Tsai MH, Lin H, Liu YW, Lee SA, Chen CC, Tsao TT, Kao CY.