Category: Assembly Tools

Pasqual 1.0 – Parallel de Novo Genome Sequence Assembler

Pasqual 1.0

:: DESCRIPTION

PASQUAL (PArallel SeQUence AssembLer) is designed for shared memory parallelism, using OpenMP due to its good tradeoff between performance and programmer productivity. Shared memory parallelism has become mainstream with the widespread production of multicore commodity processors. For PASQUAL we follow the OLC approach and use a careful combination of tailored algorithms and data structures to obtain high-quality solutions.

::DEVELOPER

Bader HPC Lab @ GeorgiaTech

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 Pasqual

:: MORE INFORMATION

Citation

Xing Liu, Pushkar R. Pande, Henning Meyerhenke, and David A. Bader.
PASQUAL: A Parallel de novo Assembler for Next Generation Genome Sequencing.
Submitted for journal publication, 2011.

Taipan 20090515 – Fast Hybrid Short-read Assembly tool

Taipan 20090515

:: DESCRIPTION

Taipan is an assembly algorithm which can be viewed as a hybrid of these two approaches. Taipan uses greedy extensions for contig construction but at each step realizes enough of the corresponding read graph to make better decisions as to how assembly should continue. We show that this approach can achieve an assembly quality at least as good as the graph-based approaches used in the popular Edena and Velvet assembly tools using a moderate amount of computing resources.

::DEVELOPER

Parallel and Distributed Architectures

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • C Compiler

:: DOWNLOAD

 Taipan

:: MORE INFORMATION

Citation

Bertil Schmidt, Ranjan Sinha, Bryan Beresford-Smith, Simon J. Puglisi:
“A Fast Hybrid Short Read Fragment Assembly Algorithm“.
Bioinformatics, 2009, 25(17): 2279-2280

 

GS De Novo Assembler – de novo DNA Sequence Assembly

GS De Novo Assembler

:: DESCRIPTION

GS De Novo Assembler (Newbler) is a software package for de novo DNA sequence assembly. It is designed specifically for assembling sequence data generated by the 454 GS-series of pyrosequencing platforms sold by 454 Life Science, a Roche diagnostic.

::DEVELOPER

454 Sequencing 

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 GS De Novo Assembler

:: MORE INFORMATION

PGAAS 1.0 – Prokaryotic Genome Assembly Assistant System

PGAAS 1.0

:: DESCRIPTION

PGAAS is prokaryotic genome assembly assistant system. The approach upon which PGAAS is based is to confirm the order of contigs and fill gaps between contigs through peptide links obtained by searching each contig end with BLASTX against protein database.

::DEVELOPER

Center for Bioinformatics, PKU.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • MySQL
  • PHP
  • Apache

:: DOWNLOAD

 PGAAS

:: MORE INFORMATION

Citation:

PGAAS: a prokaryotic genome assembly assistant system.
Yu Z, Li T, Zhao J, Luo J.
Bioinformatics. 2002 May;18(5):661-5.

SHORTY 2.0 – de novo Assembler

SHORTY 2.0

:: DESCRIPTION

SHORTY is targetted for de novo assembly of microreads with mate pair information and sequencing errors. SHORTY has some novel approach and features in addressing the short read assembly problem.

::DEVELOPER

Steven Skiena

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux / MacOsX
  • C++ Compiler

:: DOWNLOAD

 SHORTY

:: MORE INFORMATION

Citation:

BMC Bioinformatics. 2009 Jan 30;10 Suppl 1:S16.
Crystallizing short-read assemblies around seeds.
Hossain MS, Azimi N, Skiena S.

VCAKE 2.0 – Genetic Sequence Assembler

VCAKE 2.0

:: DESCRIPTION

VCAKE  (Verified Consensus Assembly by K-mer Extension) is a genetic sequence assembler capable of assembling millions of small nucleotide reads even in the presence of sequencing error. This software is currently geared towards de novo assembly of Illumina’s Solexa Sequencing data.

::DEVELOPER

the Corbin Jones Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux /  Mac OsX / Windows
  • C Compiler

:: DOWNLOAD

  VCAKE

:: MORE INFORMATION

Citation:

William R. Jeck et al.
Extending assembly of short DNA sequences to handle error
Bioinformatics (2007) 23 (21): 2942-2944.

SHARCGS – SHort read Assembler based on Robust Contig extension for Genome Sequencing

SHARCGS

:: DESCRIPTION

SHARCGS is a DNA assembly program designed for de novo assembly of 25-40mer input fragments and deep sequence coverage. Large numbers of such short reads are generated on advanced sequencing instruments.

::DEVELOPER

Max Planck Institute for Molecular Genetics

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows / MacOSX
  • Perl

:: DOWNLOAD

 SHARCGS

:: MORE INFORMATION

Citation:

Genome Res. 2007 Nov;17(11):1697-706. Epub 2007 Oct 1.
SHARCGS, a fast and highly accurate short-read assembly algorithm for de novo genomic sequencing.
Dohm JC, Lottaz C, Borodina T, Himmelbauer H.

ABACAS 1.3.1 – Algorithm Based Automatic Contiguation of Assembled Sequences

ABACAS 1.3.1

:: DESCRIPTION

ABACAS (Algorithm Based Automatic Contiguation of Assembled Sequences) is intended to rapidly contiguate (align, order, orientate), visualize and design primers to close gaps on shotgun assembled contigs based on a reference sequence.

::DEVELOPER

Thomas D. Otto

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

  ABACAS

:: MORE INFORMATION

Citation

ABACAS: algorithm-based automatic contiguation of assembled sequences.
Assefa S, Keane TM, Otto TD, Newbold C, Berriman M.
Bioinformatics. 2009 Aug 1;25(15):1968-9.