Opera 2.0.2 – Sequence Assembly Program

Opera 2.0.2

:: DESCRIPTION

Opera (Optimal Paired-End Read Assembler) is a sequence assembly program . It uses information from paired-end reads to optimally order and orient contigs assembled from shotgun-sequencing reads.

::DEVELOPER

Opera team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 Opera

:: MORE INFORMATION

Citation

J Comput Biol. 2011 Nov;18(11):1681-91. doi: 10.1089/cmb.2011.0170. Epub 2011 Sep 19.
Opera: reconstructing optimal genomic scaffolds with high-throughput paired-end sequences.
Gao S1, Sung WK, Nagarajan N.

Sequencher 5.4.1 – DNA Sequence Assembly and Analysis

Sequencher 5.4.1

:: DESCRIPTION

Sequencher is the industry standard software for DNA sequence analysis. It works with all automated sequencers and is widely known for its lightning-fast contig assembly, short learning curve, user-friendly editing tools, and superb technical support. First released almost 15 years ago, Sequencher is currently used for sequence analysis tasks in every major genomic and pharmaceutical company as well as numerous academic and government labs in over 40 countries around the world. Life Science researchers use Sequencher for many diverse DNA sequence analysis applications including de novo gene sequencing, mutation detection, forensic human identification, systematics, and more.

::DEVELOPER

Gene Codes Corporation

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / MacOsX

:: DOWNLOAD

Sequencher Demo

:: MORE INFORMATION

CISA 20140304 – Contig Integrator for Sequence Assembly

CISA 20140304

:: DESCRIPTION

CISA has been developed to integrate the assemblies into a hybrid set of contigs, resulting in assemblies of superior contiguity and accuracy, compared with the assemblies generated by the state-of-the-art assemblers and the hybrid assemblies merged by existing tools.

::DEVELOPER

CISA team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Python
  • MUMmer 3.22 or higher
  • Blast 2.2.25+ or higher

:: DOWNLOAD

 CISA

:: MORE INFORMATION

Citation

PLoS One. 2013;8(3):e60843. doi: 10.1371/journal.pone.0060843. Epub 2013 Mar 28.
CISA: contig integrator for sequence assembly of bacterial genomes.
Lin SH1, Liao YC.

SeqCons 1.0 – de novo and reference-guided Sequence Assembly

SeqCons 1.0

:: DESCRIPTION

 SeqCons (Sequence consensus) is an open source consensus computation program for Linux and Windows. The algorithm can be used for de novo and reference-guided sequence assembly.

::DEVELOPER

SeqCons Team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows

:: DOWNLOAD

 SeqCons

:: MORE INFORMATION

Citation

Rausch, T., Koren, S., Gennady, D., Weese, D., Emde, A.-K., D?ring, A., Reinert, K. (2009).
A consistency-based consensus algorithm for de novo and reference-guided sequence assembly of short reads.
Bioinformatics (2009) 25 (9): 1118-1124.

ABySS-Explorer 1.3.4 – Sequence Assembly Visualization Tool

ABySS-Explorer 1.3.4

:: DESCRIPTION

ABySS-Explorer is an interactive Java application that employs a novel graph-based representation to display a sequence assembly and associated meta data. The tool was designed with the ABySS sequence assembler in mind and was motivated by the need to examine assembly structure, in particular contig connectivity and supporting paired-end read relationships.

::DEVELOPER

Cydney Nielsen

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / Mac /  Linux
  • Java

:: DOWNLOAD

 ABySS-Explorer 

:: MORE INFORMATION

Citation

Nielsen CB, Jackman SD, Birol I, Jones SJM.
ABySS-Explorer: Visualizing genome sequence assemblies.
IEEE Transactions on Visualization and Computer Graphics (Proceedings Visualization / Information Visualization 2009). 2009. 15(6):881-8.

SAM 1.0 – Sequence Assembly Manager

SAM 1.0

:: DESCRIPTION

SAM (Sequence Assembly Manager)is a Whole Genome Assembly (WGA) Management and Visualization Tool. It provides a generic platform for manipulating, analyzing and viewing WGA data, regardless of input type.

::DEVELOPER

Kevin Teague

:: SCREENSHOTS

: REQUIREMENTS

:: DOWNLOAD

  SAM

:: MORE INFORMATION

Citation

Warren RL, Butterfield YS, Morin RD, Siddiqui AS, Marra MA, Jones SJM. (2005)
Management and Visualization of Whole Genome Shotgun Assemblies using SAM.
Biotechniques. 38:715-720

SeqAssem 200807- Molecular Sequence Assembly

SeqAssem 200807

:: DESCRIPTION

SeqAssem is a molecular sequence assembly software, proof-reading of trace file data, contig building …..

::DEVELOPER

SequentiX

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

SeqAssem

:: MORE INFORMATION

Request a free trial license to use the full spectrum of features for one month and free of charge!