GAML 0.1 – Genome Assembly by Maximum Likelihood

GAML 0.1

:: DESCRIPTION

GAML is a prototype genome assembly tool based on maximizing likelihood of the assembly in a model encompaasing error rate, insert length and other features of indvidual sequencing technologies.

:: DEVELOPER

Computational Biology @ Comenius University in Bratislava

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux

:: DOWNLOAD

GAML

:: MORE INFORMATION

Citation

GAML: genome assembly by maximum likelihood.
Boža V, Brejová B, Vinař T.
Algorithms Mol Biol. 2015 Jun 3;10:18. doi: 10.1186/s13015-015-0052-6.

MAIA 0.5 – Integrating Genome Assemblies

MAIA 0.5

:: DESCRIPTION

MAIA (Multiple Assembly IntegrAtion) is an algorithm to integrate multiple genome assemblies. For example, assemblies originating from:
– Different runs of a de novo assembler
– Assemblies of different data types
– Comparative assemblies

::DEVELOPER

The Delft Bioinformatics Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Windows / Linux / Mac OsX
Matlab
MUMmer package
GAIMC toolbox

:: DOWNLOAD

MAIA

:: MORE INFORMATION

Citation

Bioinformatics. 2010 Sep 15;26(18):i433-9.
Integrating genome assemblies with MAIA.
Nijkamp J, Winterbach W, van den Broek M, Daran JM, Reinders M, de Ridder D.

GAM – Genome Assemblies Merger

GAM

:: DESCRIPTION

GAM is a free parallel software tool to integrate two different assemblies and improves the overall quality of the genome sequences by merging them. It discovers and align similar sequences by using the positions of placed reads. An order sequence of reads contiguous on the same contig is called frame. When the same frame is shared by both original assemblies, GAM dubs it block.

::DEVELOPER

Istituto di Genomica Applicata and at University of Udine.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux

:: DOWNLOAD

GAM

:: MORE INFORMATION

Citation

A. Casagrande, C. Del Fabbro, S. Scalabrin, A. Policriti.
GAM: Genomic Assemblies Merger. A Graph Based Method to Integrate Different Assemblies
Proceedings of the Third IEEE International Conference on Bioinformatics & Biomedicine (BIBM 2009), Washington D.C. (USA), November 1-4 2009.

SEQuel 1.0.2 – Improving the Accuracy of Genome Assemblies

SEQuel 1.0.2

:: DESCRIPTION

SEQuel is a tool for improving the accuracy of high throughput sequencing assemblies.

::DEVELOPER

Roy Ronen and Christina Boucher in Pavel Pevzner’s lab at the University of California, San Diego.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux / Windows / MacOsX
Java
Perl

:: DOWNLOAD

SEQuel

:: MORE INFORMATION

Citation

R. Ronen, C. Boucher, H. Chitsaz, and P. Pevzner.
SEQuel: Improving the Accuracy of Genome Assemblies.
Bioinformatics (2012) 28 (12): i188-i196.