CGAL 0.9.6b – Computing Genome Assembly Likelihoods

CGAL 0.9.6b

:: DESCRIPTION

CGAL is a tool for computing genome assembly likelihoods. It computes the likelihood of reads with respect to the assembly and a statistical model which can be used as a metric for evaluating assemblies.

::DEVELOPER

Pachter Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

CGAL

:: MORE INFORMATION

Citation

Genome Biol. 2013 Jan 29;14(1):R8. [Epub ahead of print]
CGAL: computing genome assembly likelihoods.
Rahman A, Pachter L.

KmerGenie 1.7051 – K-mer size Selection for Genome Assembly

KmerGenie 1.7051

:: DESCRIPTION

KmerGenie estimates the best k-mer length for genome de novo assembly. Given a set of reads, KmerGenie first computes the k-mer abundance histogram for many values of k. Then, for each value of k, it predicts the number of distinct genomic k-mers in the dataset, and returns the k-mer length which maximizes this number. Experiments show that KmerGenie’s choices lead to assemblies that are close to the best possible over all k-mer lengths.

::DEVELOPER

Rayan Chikhi, Medvedev Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ Windows / MacOsX
  • R package
  • Python

:: DOWNLOAD

 KmerGenie

:: MORE INFORMATION

Citation:

Bioinformatics. 2014 Jan 1;30(1):31-7. doi: 10.1093/bioinformatics/btt310. Epub 2013 Jun 3.
Informed and automated k-mer size selection for genome assembly.
Chikhi R1, Medvedev P.

hapsembler 2.21 – Haplotype-specific Genome Assembly Toolkit

hapsembler 2.21

:: DESCRIPTION

Hapsembler is a haplotype-specific genome assembly toolkit that is designed for genomes that are rich in SNPs and other types of polymorphism. Hapsembler can be used to assemble reads from a variety of platforms including Illumina and Roche/454.

::DEVELOPER

Nilgun Donmez and Michael Brudno

:: SCREENSHOTS

N/A

::REQUIREMENTS

  • Linux
  • Perl

:: DOWNLOAD

  hapsembler

:: MORE INFORMATION

Citation

Nilgun Donmez and Michael Brudno (2011)
Hapsembler: an assembler for highly polymorphic genomes.
In Proceedings of the 15th Annual international conference on Research in computational molecular biology (RECOMB’11), Springer-Verlag, Berlin, Heidelberg, 38-52.

GMASS – Genome Assembly Structural Similarity

GMASS

:: DESCRIPTION

The GMASS score is a novel measure for representing structural similarity between two assemblies. It represents the structural similarity of a pair of assemblies based on the length and number of similar genomic regions defined as consensus segment blocks (CSBs) in the assemblies.

::DEVELOPER

Bioinformatics Laboratory, Konkuk University

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Perl

:: DOWNLOAD

GMASS

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2019 Mar 18;20(1):147. doi: 10.1186/s12859-019-2710-z.
GMASS: a novel measure for genome assembly structural similarity.
Kwon D, Lee J, Kim J.

Cortex 1.05.21 – Genome Assembly and Variation Analysis

Cortex 1.05.21

:: DESCRIPTION

Cortex is an efficient and low-memory software framework for analysis of genomes using sequence data. There are two main executables, being developed in parallel streams: cortex_con (primary contact Mario Caccamo) is for consensus genome assembly, and cortex_var (primary contact Zamin Iqbal) is for variation and population assembly.

::DEVELOPER

Cortex team

:: SCREENSHOTS

N/a

:: REQUIREMENTS

  • Linux
  • C compiler

:: DOWNLOAD

 Cortex

:: MORE INFORMATION

Citation

Nat Genet. 2012 Jan 8;44(2):226-32. doi: 10.1038/ng.1028.
De novo assembly and genotyping of variants using colored de Bruijn graphs.
Iqbal Z, Caccamo M, Turner I, Flicek P, McVean G.

Circlator 1.5.6 – A tool to Circularize Genome Assemblies

Circlator 1.5.6

:: DESCRIPTION

Circlator is the first tool to automate assembly circularization and produce accurate linear representations of circular sequences.

::DEVELOPER

Pathogen Informatics, Wellcome Trust Sanger Institute

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux /  MacOsX
  • Python
  • BWA version >= 0.7.12
  • prodigal version >= 2.6
  • SAMtools (version 0.1.9 or 1.2)
  • MUMmer version >= 3.23
  • SPAdes version 3.5.0, 3.6.0 or 3.6.2

:: DOWNLOAD

 Circlator

:: MORE INFORMATION

Citation

Circlator: automated circularization of genome assemblies using long sequencing reads.
Hunt M, Silva ND, Otto TD, Parkhill J, Keane JA, Harris SR.
Genome Biol. 2015 Dec 29;16(1):294. doi: 10.1186/s13059-015-0849-0.

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.

QUAST 4.1 – Quality Assessment Tool for Genome Assemblies

QUAST 4.1

:: DESCRIPTION

QUAST evaluates a quality of genome assemblies by computing various metrics and providing nice reports.

MetaQUAST evaluates and compares metagenome assemblies based on alignments to close references.

Icarus is a novel genome visualizer for accurate assessment and analysis of genomic draft assemblies, which is based on QUAST genome quality assessment tool

::DEVELOPER

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

:: SCREENSHOTS

MetaQUAST

:: REQUIREMENTS

  • Linux /  MacOsX
  • Python
  • Perl
  • MUMmer

:: DOWNLOAD

 QUAST

:: MORE INFORMATION

Citation

Icarus: visualizer for de novo assembly evaluation.
Mikheenko A, Valin G, Prjibelski A, Saveliev V, Gurevich A.
Bioinformatics. 2016 Jul 4. pii: btw379.

MetaQUAST: evaluation of metagenome assemblies.
Mikheenko A, Saveliev V, Gurevich A.
Bioinformatics. 2015 Nov 26. pii: btv697

Alexey Gurevich, Vladislav Saveliev, Nikolay Vyahhi and Glenn Tesler
QUAST: quality assessment tool for genome assemblies
Bioinformatics volume 29, issue 8, pp. 1072-1075.

GATB 1.1.1 – Genome Assembly & Analysis Tool Box

GATB 1.1.1

:: DESCRIPTION

GATB provides an easy way to develop efficient and fast NGS tools. GATB is a C++ library of high level functions designed to benefit from recent advances in NGS data structures for handling huge datasets of sequencing data.

::DEVELOPER

GATB team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX

:: DOWNLOAD

 GATB

:: MORE INFORMATION

Citation:

GATB: Genome Assembly & Analysis Tool Box.
Drezen E, Rizk G, Chikhi R, Deltel C, Lemaitre C, Peterlongo P, Lavenier D.
Bioinformatics. 2014 Jul 1. pii: btu406