RNAssess – Quality Assessment of RNA 3D Structures

RNAssess

:: DESCRIPTION

RNAssess is a computational server for comparison of RNA 3D models with the reference structure and for discrimination between the correct and incorrect models.

::DEVELOPER

The Bioinformatics Group, Poznan University of Technology.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

RNAssess-a web server for quality assessment of RNA 3D structures.
Lukasiak P, Antczak M, Ratajczak T, Szachniuk M, Popenda M, Adamiak RW, Blazewicz J.
Nucleic Acids Res. 2015 Jun 11. pii: gkv557.

ModelEvaluator 1.0 – Quality Assessment of a Single Model

ModelEvaluator 1.0

:: DESCRIPTION

ModelEvaluator is a program to evaluate the quality of a single protein model using support vector machines and 1D and 2D structural features

::DEVELOPER

Dr. Jianlin Cheng

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

  ModelEvaluator

:: MORE INFORMATION

Citation

Z. Wang, A.N. Tegge and J. Cheng.
Evaluating the Absolute Quality of a Single Protein Model Using Support Vector Machines and Structural Features.
Proteins,vol. 75, no. 3, 638-647, 2009.

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.

SolexaQA 3.1.4 – Quality Assessment of Illumina Second-generation Sequencing data

SolexaQA 3.1.4

:: DESCRIPTION

SolexaQA is a software package to calculate sequence quality statistics and create visual representations of data quality for Illumina’s second-generation sequencing technology (historically known as “Solexa”).

::DEVELOPER

Associate Professor Murray Cox, Massey University

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/
  • R package
  • Perl 

:: DOWNLOAD

 SolexaQA

:: MORE INFORMATION

Citation

Cox, M.P., D.A. Peterson, and P.J. Biggs. 2010.
SolexaQA: At-a-glance quality assessment of Illumina second-generation sequencing data.
BMC Bioinformatics 11:485

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.

ConQuass – Quality Assessment of Protein Model-Structures using Evolutionary Conservation

ConQuass

:: DESCRIPTION

ConQuass is a novel quality assessment program based on the consistency between the model structure and the protein’s conservation pattern.

::DEVELOPER

The Ben-Tal Lab of Computational Structural Biology

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux
  • Perl
  • R
:: DOWNLOAD

 ConQuass

:: MORE INFORMATION

Citation:

Bioinformatics. 2010 May 15;26(10):1299-307. doi: 10.1093/bioinformatics/btq114. Epub 2010 Apr 12.
Quality assessment of protein model-structures using evolutionary conservation.
Kalman M1, Ben-Tal N.

Admixem v1.0.1 – Quality Assessment Tool for Metagenome Assemblies

Admixem v1.0.1

:: DESCRIPTION

Admix’em (Admixture simulator) is a new forward-time simulator that allows for rapid and realistic simulations of admixed populations with selection.

::DEVELOPER

Ray Cui

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux /  MacOsX
  • C++ COmpiler

:: DOWNLOAD

 Admixem

:: MORE INFORMATION

Citation

Admix’em: A flexible framework for forward-time simulations of hybrid populations with selection and mate choice.
Cui R, Schumer M, Rosenthal GG.
Bioinformatics. 2015 Nov 28. pii: btv700.

ArrayExpressHTS 1.18.0 – RNA-seq data Processing and Quality Assessment

ArrayExpressHTS 1.18.0

:: DESCRIPTION

ArrayExpressHTS is an R and Bioconductor RNA-seq processing pipeline that highly utilizes distributed computing for data processing and quality assessment of High-Throughput Sequencing experiments and datasets

::DEVELOPER

EBI.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows / MacOsX
  • R package
  • Bioconductor

:: DOWNLOAD

  ArrayExpressHTS

:: MORE INFORMATION

Citation:

Bioinformatics. 2011 Mar 15;27(6):867-9. doi: 10.1093/bioinformatics/btr012. Epub 2011 Jan 13.
A pipeline for RNA-seq data processing and quality assessment.
Goncalves A, Tikhonov A, Brazma A, Kapushesky M.

TEQC 3.8.0 – Quality Assessment of Target Enrichment Experiments

TEQC 3.8.0

:: DESCRIPTION

TEQC is an R/Bioconductor package for quality assessment of target enrichment experiments.

::DEVELOPER

Bioinformatics Core @ CRG

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ MacOsX/Windows
  • R package
  • BioConductor

:: DOWNLOAD

 TEQC

:: MORE INFORMATION

Citation

Bioinformatics. 2011 May 1;27(9):1316-7. doi: 10.1093/bioinformatics/btr122.
TEQC: an R package for quality control in target capture experiments.
Hummel M, Bonnin S, Lowy E, Roma G.

MeQA 1.0 – Pipeline for MeDIP-seq Data Quality Assessment and Analysis

MeQA 1.0

:: DESCRIPTION

MeQA is a pipeline for the pre-processing, quality assessment, read distribution and methylation estimation for MeDIP-sequence datasets.

::DEVELOPER

MeQA team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Python

:: DOWNLOAD

 MeQA

:: MORE INFORMATION

Citation

Bioinformatics. 2012 Feb 15;28(4):587-8. doi: 10.1093/bioinformatics/btr699. Epub 2011 Dec 22.
MeQA: a pipeline for MeDIP-seq data quality assessment and analysis.
Huang J1, Renault V, Sengenès J, Touleimat N, Michel S, Lathrop M, Tost J.