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.

ABySS 2.1.5 – de novo, parallel, paired-end Sequence Assembler

ABySS 2.1.5

:: DESCRIPTION

ABySS (Assembly By Short Sequences) is a de novo, parallel, paired-end sequence assembler that is designed for short reads. The single-processor version is useful for assembling genomes up to 100 Mbases in size. The parallel version is implemented using MPI and is capable of assembling larger genomes.

::DEVELOPER

Canada’s Michael Smith Genome Sciences Centre

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/Windows/MacOsX

:: DOWNLOAD

 ABySS

:: MORE INFORMATION

Citation

Simpson JT, Wong K, Jackman SD, Schein JE, Jones SJ, Birol I.
ABySS: A parallel assembler for short read sequence data.
Genome Res. 2009. 19: 1117-1123

SVDetect 0.8b – Detect Genomic Structural Variations from Paired-end and Mate-pair Sequencing data

SVDetect 0.8b

:: DESCRIPTION

SVDetect is a application for the isolation and the type prediction of intra- and inter-chromosomal rearrangements from paired-end/mate-pair sequencing data provided by the high-throughput sequencing technologies.

::DEVELOPER

Boeva lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 SVDetect

:: MORE INFORMATION

Citation:

Bioinformatics. 2010 Aug 1;26(15):1895-6.
SVDetect: a tool to identify genomic structural variations from paired-end and mate-pair sequencing data.
Zeitouni B, Boeva V, Janoueix-Lerosey I, Loeillet S, Legoix-né P, Nicolas A, Delattre O, Barillot E.

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.

DELLY 0.7.3 – integrated Split-read and Paired-end based Structural Variant Discovery in Deep sequencing data

DELLY 0.7.3

:: 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

misFinder v0.4.05.05 – Identify Mis-assemblies in an unbiased manner using Reference and Paired-end Reads

misFinder v0.4.05.05

:: DESCRIPTION

misFinder is a tool that aims to identify the assembly errors with high accuracy in an unbiased way and correct these errors at their mis-assembled positions to improve the assembly accuracy for downstream analysis.

::DEVELOPER

misFinder team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 misFinder

:: MORE INFORMATION

Citation

misFinder: identify mis-assemblies in an unbiased manner using reference and paired-end reads.
Zhu X, Leung HC, Wang R, Chin FY, Yiu SM, Quan G, Li Y, Zhang R, Jiang Q, Liu B, Dong Y, Zhou G, Wang Y.
BMC Bioinformatics. 2015 Nov 16;16(1):386.

SpliceTrap 0.95 – Exon Inclusion Ratio Estimation from Paired End RNAseq data

SpliceTrap 0.95

:: DESCRIPTION

SpliceTrap is a statistic tool for quantifying exon inclusion ratios in paired-end RNA-seq data, with broad applications for the study of alternative splicing. SpliceTrap approaches to exon inclusion level estimation as a Bayesian inference problem. For every exon it quantifies the extent to which it is included, skipped or subjected to size variations due to alternative 3’/5’ splice sites or Intron Retention. In addition, SpliceTrap can quantify alternative splicing within a single cellular condition, with no need of a background set of reads.

::DEVELOPER

Jie Wu

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 SpliceTrap

:: MORE INFORMATION

Citation:

Wu J, Akerman M, Sun S, McCombie WR, Krainer AR, Zhang MQ (2011)
SpliceTrap: a method to quantify alternative splicing under single cellular conditions:
Bioinformatics 27, 3010-3016, doi:10.1093/bioinformatics/btr508

PANDASEQ 2.8 / Pandaseq-sam 1.3 – PAired-eND Assembler for DNA sequences

PANDASEQ 2.8 / Pandaseq-sam 1.3

:: DESCRIPTION

PANDASEQ is a program to align Illumina reads, optionally with PCR primers embedded in the sequence, and reconstruct an overlapping sequence.

PANDASEQ-SAM is a program to align Illumina reads, optionally with PCR primers embedded in the sequence, and reconstruct an overlapping sequence. This version works on SAM/BAM formatted files.

::DEVELOPER

Andre P Masella , Josh D. Neufeld

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX/ Windows
  • C Compiler 

:: DOWNLOAD

 PANDASEQ , PANDASEQ-SAM

:: MORE INFORMATION

Citation

Andre P Masella, Andrea K Bartram, Jakub M Truszkowski, Daniel G Brown and Josh D Neufeld.
PANDAseq: paired-end assembler for illumina sequences.
BMC Bioinformatics 2012, 13:31.