SWAP-Assembler 2 – A scalable and fully parallelized Genome Assembler

SWAP-Assembler 2

:: DESCRIPTION

SWAP-Assembler (Small World Asynchronous Parallel model) is a scalable and fully parallelized genome assembler designed for massive sequencing data.

::DEVELOPER

SWAP-Assembler team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 SWAP-Assembler

:: MORE INFORMATION

Citation:

SWAP-Assembler: scalable and efficient genome assembly towards thousands of cores.
Meng J, Wang B, Wei Y, Feng S, Balaji P.
BMC Bioinformatics. 2014;15 Suppl 9:S2. doi: 10.1186/1471-2105-15-S9-S2.

SPAdes 3.6.2 – Single-cell Genome Assembler

SPAdes 3.6.2

:: DESCRIPTION

SPAdes (St. Petersburg genome assembler) is intended for both standard isolates and single-cell MDA bacteria assemblies.

::DEVELOPER

Algorithmic Biology Lab at St. Petersburg Academic University of the Russian Academy of Sciences

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux /  MacOsX
  • Python

:: DOWNLOAD

 SPAdes

:: MORE INFORMATION

Citation

hybridSPAdes: an algorithm for hybrid assembly of short and long reads.
Antipov D, Korobeynikov A, McLean JS, Pevzner PA.
Bioinformatics. 2015 Nov 20. pii: btv688

Anton Bankevich,et al.
SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing.
Journal of Computational Biology 19(5) (2012), 455-477. doi:10.1089/cmb.2012.0021

KGBassembler 1.2 – Karyotype-based Genome Assembler for Brassicaceae Species

KGBassembler 1.2

:: DESCRIPTION

KGBassembler (Brassicaceae genome assembler) is a C++ based tool for assembling contigs and/or scaffolds to full chromosomes based on the karyotype maps of Brassicaceae species and without the need of genetic and physical maps.

::DEVELOPER

Wanglab

:: SCREENSHOTS

KGBassembler

:: REQUIREMENTS

  • Windows/Linux

:: DOWNLOAD

 KGBassembler

 :: MORE INFORMATION

Citation

Bioinformatics. 2012 Dec 1;28(23):3141-3. doi: 10.1093/bioinformatics/bts586. Epub 2012 Oct 7.
KGBassembler: a karyotype-based genome assembler for Brassicaceae species.
Ma C1, Chen H, Xin M, Yang R, Wang X.

AutoAssemblyD 0.1 – Graphical User Interface system for several Genome Assembler

AutoAssemblyD 0.1

:: DESCRIPTION

The AssemblyD is a software which performed the local and remote genome assembly by several assemblers based on an XML Template which can replace the large command lines required by most assemblers.

::DEVELOPER

AutoAssemblyD team

:: SCREENSHOTS

AutoAssemblyD

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • Java

:: DOWNLOAD

 AutoAssemblyD

:: MORE INFORMATION

Citation

Bioinformation. 2013 Sep 23;9(16):840-1. doi: 10.6026/97320630009840. eCollection 2013.
AutoAssemblyD: a graphical user interface system for several genome assemblers.
Veras AA1, de Sá PH, Azevedo V, Silva A, Ramos RT.

PRICE 1.2 – de novo Genome Assembler

PRICE 1.2

:: DESCRIPTION

PRICE (Paired-Read Iterative Contig Extension) is a de novo genome assembler implemented in C++. Its name describes the strategy that it implements for genome assembly: PRICE uses paired-read information to iteratively increase the size of existing contigs. Initially, those contigs can be individual reads from a subset of the paired-read dataset, non-paired reads from sequencing technologies that provide non-paired data, or contigs that were output from a prior run of PRICE or any other assembler.

::DEVELOPER

DeRisi LabUCSF

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • C++ Compiler

:: DOWNLOAD

 PRICE

:: MORE INFORMATION

Citation

PRICE: Software for the Targeted Assembly of Components of (Meta)Genomic Sequence Data
J. Graham Ruby, Priya Bellare and Joseph L. DeRisi
G3 March 23, 2013 g3.113.005967

PEAssember 1.2 – A de novo Genome Assembler

PEAssember 1.2

:: DESCRIPTION

PEAssember is a parallel de novo genome assembler for small – mid sized genomes.

::DEVELOPER

Pramila Nuwantha Ariyaratne, Sung Wing Kin, Ken

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ Windows/ MacOsX
  • C++ Compiler

:: DOWNLOAD

 PEAssember

:: MORE INFORMATION

Citation

Bioinformatics. 2011 Jan 15;27(2):167-74. doi: 10.1093/bioinformatics/btq626. Epub 2010 Dec 12.
PE-Assembler: de novo assembler using short paired-end reads.
Ariyaratne PN, Sung WK.