RACER 1.0.1 – Rapid and Accurate Correction of Errors in Reads

RACER 1.0.1

:: DESCRIPTION

RACER is a C++/OpenMP program that corrects sequencing errors in high-throughput DNA sequencing data, especially designed for the Illumina platform.

::DEVELOPER

LUCIAN ILIE

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 RACER

:: MORE INFORMATION

Citation

Bioinformatics. 2013 Oct 1;29(19):2490-3. doi: 10.1093/bioinformatics/btt407. Epub 2013 Jul 12.
RACER: Rapid and accurate correction of errors in reads.
Ilie L1, Molnar M.

TS4MSBH – Tabu search algorithm for DNA Sequencing by Hybridization problem

TS4MSBH

:: DESCRIPTION

TS4MSBH is a tabu search algorithm for DNA sequencing by hybridization problem with a partial multiplicity information (a test set included)

::DEVELOPER

The Bioinformatics Group, Poznan University of Technology.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows
  • .NET Framework 3.5

:: DOWNLOAD

 TS4MSBH

 :: MORE INFORMATION

Tabusearch – DNA Sequencing by Hybridization with Isothermic Libraries

Tabusearch

:: DESCRIPTION

Tabusearch is a sofrware for DNA sequencing by hybridization with isothermic libraries.

::DEVELOPER

The Bioinformatics Group, Poznan University of Technology.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

 Tabusearch

:: MORE INFORMATION

Citation

J. Blazewicz, P. Formanowicz, M. Kasprzak, W.T. Markiewicz, A. Swiercz,
Tabu search algorithm for DNA sequencing by hybridization with isothermic libraries“,
Computational Biology and Chemistry 28, 2004, pp. 11-19.

SeqControl 1.0.3 – Process Control for DNA Sequencing

SeqControl 1.0.3

:: DESCRIPTION

SeqControl is a set of Perl and R scripts designed to assess the quality of sequencing data using multiple quality metrics.

::DEVELOPER

Boutros Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • R
  • Perl

:: DOWNLOAD

 SeqControl

:: MORE INFORMATION

Citation:

SeqControl: process control for DNA sequencing.
Chong LC, Albuquerque MA, Harding NJ, Caloian C, Chan-Seng-Yue M, de Borja R, Fraser M, Denroche RE, Beck TA, van der Kwast T, Bristow RG, McPherson JD, Boutros PC.
Nat Methods. 2014 Oct;11(10):1071-5. doi: 10.1038/nmeth.3094

Ray 2.3.1 – Parallel Genome Assemblies for Parallel DNA sequencing

Ray 2.3.1

:: DESCRIPTION

Ray is a parallel software that computes de novo genome assemblies with next-generation sequencing data.

::DEVELOPER

Sébastien Boisvert

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/Mac OsX/Windows
  • C++ Compiler

:: DOWNLOAD

 Ray

:: MORE INFORMATION

Citation

Genome Biol. 2012 Dec 22;13(12):R122. doi: 10.1186/gb-2012-13-12-r122.
Ray Meta: scalable de novo metagenome assembly and profiling.
Boisvert S, Raymond F, Godzaridis E, Laviolette F, Corbeil J.

Ray: simultaneous assembly of reads from a mix of high-throughput sequencing technologies.
Boisvert S, Laviolette F, Corbeil J.
Journal of Computational Biology November 2010, 17(11): 1519-1533.

CRISP 20131227 – Detection of SNVs and Short Insertion/deletion variants from Pooled high throughput DNA sequencing data

CRISP 20131227

:: DESCRIPTION

CRISP (Comprehensive Read analysis for Identification of Single Nucleotide Polymorphisms from Pooled sequencing) is a software program to detect SNPs and short indels from pooled sequencing data generated using next-generation sequencing instruments. CRISP is designed to detect both rare and common variants by utilizing sequence reads from next-generation sequencing of multiple DNA pools.

::DEVELOPER

Vikas Bansal

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  •  Linux

:: DOWNLOAD

 CRISP 

:: MORE INFORMATION

Citation

Bioinformatics. 2010 Jun 15;26(12):i318-24. doi: 10.1093/bioinformatics/btq214.
A statistical method for the detection of variants from next-generation resequencing of DNA pools.
Bansal V.

SeqTrace 0.9.0 – Rapidly Processing DNA Sequencing Chromatograms

SeqTrace 0.9.0

:: DESCRIPTION

SeqTrace is an application for viewing and processing DNA sequencing chromatograms (trace files). SeqTrace makes it easy to quickly generate high-quality finished sequences from a large number of trace files. SeqTrace can automatically identify, align, and compute consensus sequences from matching forward and reverse traces, filter low-quality base calls, and perform end trimming of finished sequences. The finished DNA sequences can then be exported to common sequence file formats, such as FASTA.

::DEVELOPER

Brian J. Stucky  stuckyb@colorado.edu , Guralnick Lab

:: SCREENSHOTS

SeqTrace 

:: REQUIREMENTS

  • Linux/ MacOsX/ Windows 
  • Python
  • PyGTK with the GTK+

:: DOWNLOAD

 SeqTrace

:: MORE INFORMATION

Citation

J Biomol Tech. 2012 Sep;23(3):90-3. doi: 10.7171/jbt.12-2303-004.
SeqTrace: a graphical tool for rapidly processing DNA sequencing chromatograms.
Stucky BJ.

CpGviewer 20110406 – Interactive Data Analysis in Bisulphite DNA Sequencing

CpGviewer 20110406

:: DESCRIPTION

CpGviewer is designed to speed up the characterisation of mammalian CpG islands by aligning DNA sequences from bisulphite-modified DNA to the genomic sequence of the CpG island. While simple in principle, this is a tedious error-prone task when done manually

::DEVELOPER

Leeds Institute of Molecular Medicine

:: SCREENSHOTS

CpGviewer

:: REQUIREMENTS

  • Windows
  • Microsoft .NET framework version 2.0

:: DOWNLOAD

 CpGviewer

:: MORE INFORMATION

Citation

Carr IM, Valleley EMA, Cordery SF, Markham AF & Bonthron DT (2007).
Sequence analysis and editing for bisulphite genomic sequencing projects.
Nucleic Acids Res., 35:e79.