Tag: Paired End Read

Pairoscope 0.4.2 – Display of Paired End Reads

Pairoscope 0.4.2

:: DESCRIPTION

Pairoscope (formerly Yenta) was developed as a quick and simple way to generate diagrams indicating the relationship of paired end sequencing reads. It functions by displaying multiple genomic regions, their read depth at each base in the region and arcs within or between regions to indicate pairing information. Currently, Pairoscope supports the graphing of multiple regions, but they must be at different locations: the behavior of Pairoscope is undefined if attempting to graph the same region twice. It uses a bam file as input, and color codes the read pair graph to reflect different types of abnormally oriented reads. Individual reads are represented as vertical lines drawn at the genomic location where the read mapped.

::DEVELOPER

The Genome Institute

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • C Complier

:: DOWNLOAD

 Pairoscope

:: MORE INFORMATION

casper 2.26.0 – Characterization of Alternative Splicing based on Paired-End Reads

casper 2.26.0

:: DESCRIPTION

Casper is an R package for infering alternative splicing from paired-end RNA-seq data

::DEVELOPER

David Rossell <rosselldavid at gmail.com>, Camille Stephan-Otto, Manuel Kroiss, Miranda Stobbe, Victor Pena

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Mac OsX / Windows
  • R

:: DOWNLOAD

 Casper

:: MORE INFORMATION

Citation

Designing alternative splicing RNA-seq studies. Beyond generic guidelines.
Stephan-Otto Attolini C, Peña V, Rossell D.
Bioinformatics. 2015 Jul 27. pii: btv436

CASPER 0.8.2 – Context-Aware Scheme for Paired-End Read

CASPER 0.8.2

:: DESCRIPTION

CASPER is a state-of-the art merging tool in terms of accuracy and robustness. Using this sophisticated merging method, we could get elongated reads from the forward and reverse reads.

::DEVELOPER

Data Science Laboratory, Seoul National University.

:: SCREENSHOTS

n/a

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 CASPER

:: MORE INFORMATION

Citation:

BMC Bioinformatics. 2014;15 Suppl 9:S10. doi: 10.1186/1471-2105-15-S9-S10. Epub 2014 Sep 10.
CASPER: context-aware scheme for paired-end reads from high-throughput amplicon sequencing.
Kwon S, Lee B, Yoon S.

ELOPER 1.2 – Elongation of Paired-end Reads for de novo Assembly

ELOPER 1.2

:: DESCRIPTION

ELOPER is a pre-processing tool for pair-end sequences that produces a better read library for assembly programs.

::DEVELOPER

YanaiLab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux
  • Perl / C++ Compiler

:: DOWNLOAD

 ELOPER

:: MORE INFORMATION

Citation:

ELOPER: elongation of paired-end reads as a pre-processing tool for improved de novo genome assembly.
Silver DH, Ben-Elazar S, Bogoslavsky A, Yanai I.
Bioinformatics. 2013 Jun 1;29(11):1455-7. doi: 10.1093/bioinformatics/btt169.

BreakPointer Beta – Pinpoint Rearrangement Breakpoints using Paired end reads

BreakPointer Beta

:: DESCRIPTION

BreakPointer is a tool to pinpoint rearrangement breakpoints using paired end reads

::DEVELOPER

The Cancer Genome Analysis (CGA) group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

  BreakPointer

:: MORE INFORMATION

Citation

Drier Y, Lawrence MS, Carter SL, Stewart C, Gabriel SB, Lander ES, Meyerson M, Beroukhim R, Getz G.
Somatic rearrangements across cancer reveal classes of samples with distinct patterns of DNA breakage and rearrangement-induced hypermutability.
Genome Research 2012. Published in Advance November 2, 2012, doi:10.1101/gr.141382.112

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