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

TGNet – Visualization and Quality Assessment of de novo Genome Assemblies

TGNet

:: DESCRIPTION

TGNet is a Cytoscape-based tool for visualization and quality assessment of de novo genome assemblies. Specifically it facilitates rapid detection of inconsistencies between a genome assembly and an independently derived transcriptome assembly.

::DEVELOPER

Wurm Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Java
  • Cytoscape

:: DOWNLOAD

 TGNet

:: MORE INFORMATION

Citation

Bioinformatics. 2011 Dec 15;27(24):3425-6. doi: 10.1093/bioinformatics/btr569. Epub 2011 Oct 12.
Visualization and quality assessment of de novo genome assemblies.
Riba-Grognuz O, Keller L, Falquet L, Xenarios I, Wurm Y.

KmerGenie 1.6982 – K-mer size Selection for Genome Assembly

KmerGenie 1.6682

:: 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, Paul Medvedev

:: 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.

REAPR 1.0.18 – Genome Assembly Evaluation

REAPR 1.0.18

:: DESCRIPTION

REAPR (Recognising Errors in Assemblies using Paired Reads) is a tool that evaluates the accuracy of a genome assembly using mapped paired end reads, without the use of a reference genome for comparison. It can be used in any stage of an assembly pipeline to automatically break incorrect scaffolds and flag other errors in an assembly for manual inspection. It reports mis-assemblies and other warnings, and produces a new broken assembly based on the error calls.

::DEVELOPER

REAPR  team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 REAPR

:: MORE INFORMATION

Citation:

REAPR: a universal tool for genome assembly evaluation.
Hunt M, Kikuchi T, Sanders M, Newbold C, Berriman M, Otto TD.
Genome Biol. 2013 May 27;14(5):R47