Scaffold_builder v2.2 – Order Contigs generated by draft sequencing along a Reference Sequence

Scaffold_builder v2.2

:: DESCRIPTION

Scaffold_builder is software to order contigs generated by draft sequencing along a reference sequence. Gaps are filled with N’s and small overlaps are aligned with Muscle and the consensus created with IUPAC codes. Scaffold_builder can help in the assembly and annotation of genomes by revealing what is missing and allowing targeted sequencing to close those gaps.

::DEVELOPER

the Edwards Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

  Scaffold_builder

:: MORE INFORMATION

Citation

Source Code Biol Med. 2013 Nov 22;8(1):23. doi: 10.1186/1751-0473-8-23.
Combining de novo and reference-guided assembly with scaffold_builder.
Silva GG1, Dutilh BE, Matthews TD, Elkins K, Schmieder R, Dinsdale EA, Edwards RA.

Atlas-Link 0.01 – Link Genome Sequence Contigs into Scaffold

Atlas-Link 0.01

:: DESCRIPTION

Atlas-Link links and orients genome sequence contigs into scaffolds quickly and accurately using mate-pair information. Atlas-Link can also be used to superscaffold existing genome assemblies with data from new sequencing technologies.

::DEVELOPER

Human Genome Sequencing Center, Baylor College of Medicine

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 Atlas-Link

:: MORE INFORMATION

Contiguity 1.0.4 – Contig Adjacency Graph Construction and Visualisation

Contiguity 1.0.4

:: DESCRIPTION

Contiguity is interactive software for the visualization and manipulation of de novo genome assemblies.

::DEVELOPER

Mitchell J Sullivan

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • Python

:: DOWNLOAD

 Contiguity

:: MORE INFORMATION

ScaffoldScaffolder 0.1 – Solving Contig Orientation via Bidirected to Directed Graph Reduction

ScaffoldScaffolder 0.1

:: DESCRIPTION

ScaffoldScaffolder is a stand-alone scaffolding algorithm which was designed specifically for scaffolding diploid genomes.

::DEVELOPER

Computational Science Laboratory 

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • JAVA

:: DOWNLOAD

 ScaffoldScaffolder

:: MORE INFORMATION

Citation:

BMC Bioinformatics. 2015;16 Suppl 7:S5. doi: 10.1186/1471-2105-16-S7-S5. Epub 2015 Apr 23.
Heterozygous genome assembly via binary classification of homologous sequence.
Bodily PM, Fujimoto M, Ortega C, Okuda N, Price JC, Clement MJ, Snell Q.

ScaffoldScaffolder: Solving Contig Orientation via Bidirected to Directed Graph Reduction.
Bodily PM, Fujimoto MS, Snell Q, Ventura D, Clement MJ.
Bioinformatics. 2015 Sep 17. pii: btv548.

GMcloser 1.5.1 / GMvalue 1.3 – Closing the Gaps in Scaffolds with Preassembled Contigs

GMcloser 1.5.1 / GMvalue 1.3

:: DESCRIPTION

GMcloser fills and closes the gaps present in scaffold assemblies, especially those generated by the de novo assembly of whole genomes with next-generation sequencing (NGS) reads.

GMvalue is a tool to determine misassembly sites in contigs and scaffolds.

::DEVELOPER

GMcloser team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 GMcloser / GMvalue

:: MORE INFORMATION

Citation

GMcloser: closing gaps in assemblies accurately with a likelihood-based selection of contig or long-read alignments.
Kosugi S, Hirakawa H, Tabata S.
Bioinformatics. 2015 Aug 10. pii: btv465.

CAR – Contig Assembly of Prokaryotic Draft Genomes Using Rearrangements

CAR

:: DESCRIPTION

CAR is an efficient and more accurate tool for assembling contigs of a prokaryotic draft genome based on a reference genome.

::DEVELOPER

Algorithm and Bioinformatics Laboratory, Department of Computer Science, National Tsing Hua University, Taiwan

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 CAR

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2014 Nov 28;15(1):381.
CAR: contig assembly of prokaryotic draft genomes using rearrangements.
Lu C, Chen KT, Huang SY, Chiu HT.

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.

Projector 2 – Automatic Contig Mapping for Gap Closure purposes

Projector 2

:: DESCRIPTION

Projector was designed for automatic positioning of contigs from an unfinished prokaryotic genome on a template genome of a closely related strain or species

::DEVELOPER

Sacha A.F.T. van Hijum (svhijum@cmbi.ru.nl) , Aldert L. Zomer, Oscar P. Kuipers, and Jan Kok

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • WEb Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W560-6.
Projector 2: contig mapping for efficient gap-closure of prokaryotic genome sequence assemblies.
van Hijum SA1, Zomer AL, Kuipers OP, Kok J.

Sacha A. F. T. van Hijum, Aldert L. Zomer, Oscar P. Kuipers and Jan Kok
Projector: automatic contig mapping for gap closure purposes
Nucl. Acids Res. (2003) 31 (22): e144.

SimAssemblyStage1/2 0.2 – Assembly Alignment of Contigs

SimAssemblyStage1/2 0.2

:: DESCRIPTION

SimAssemblyStage1: Perfectly aligns TranscriptSimulator reads to their nucleotide templates using read title inforamation, creating ideal simulated assembly of super contigs.

SimAssemblyStage2: Creates an optimal simulated assembly alignment of contigs using the output of SimAssemblyStage1.

::DEVELOPER

J. Cris Vera

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

 SimAssemblyStage1/2

:: MORE INFORMATION

G4ALL 1.0.4 – Graphic Contig Analyzer for All Sequencing Platforms

G4ALL 1.0.4

:: DESCRIPTION

G4ALL is a stand-alone tool that facilitates the editing of the contigs generated by assembly process. G4ALL use mapping results produced by Blast or Mummer against a reference genome to generate a scaffold based on the overlap of the contigs after curation. Besides providing information on the gene products contained in each contig, obtained through a search of the available biological databases which can be inserted in G4ALL database.

::DEVELOPER

Dr. Rommel Ramos – rommelramos@ufpa.br

:: SCREENSHOTS

G4ALL

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • Java

:: DOWNLOAD

 G4ALL

:: MORE INFORMATION

Citation

Bioinformation. 2013 Jun 29;9(11):599-604. doi: 10.6026/97320630009599. Print 2013.
Graphical contig analyzer for all sequencing platforms (G4ALL): a new stand-alone tool for finishing and draft generation of bacterial genomes.
Ramos RT1, Carneiro AR, Caracciolo PH, Azevedo V, Schneider MP, Barh D, Silva A.