QUAST 5.1.0 – Quality Assessment Tool for Genome Assemblies

QUAST 5.1.0

:: 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

:: SCREENSHOTS

:: 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.

QPLOT 20130627 – Quality Assessment and Diagnosis tool for Sequencing

QPLOT 20130627

:: DESCRIPTION

QPLOT calculates various summary statistics some of which are plotted in a PDF file. These statistics can be used to assess the sequencing quality of sequence reads and include empirical base quality scores, GC biases, insert size distribution, depth distribution, genome coverage, empirical Q20 count, and so on.

::DEVELOPER

QPLOT team

:: SCREENSHOTS

N/A

::REQUIREMENTS

Linux

:: DOWNLOAD

QPLOT

:: MORE INFORMATION

Citation

Bingshan Li, Xiaowei Zhan, Mary-Kate Wing, Paul Anderson, Hyun Min Kang, and Goncalo R. Abecasis,
“QPLOT: A Quality Assessment Tool for Next Generation Sequencing Data,”
BioMed Research International, vol. 2013, Article ID 865181, 4 pages, 2013. doi:10.1155/2013/865181

SSP 1.2.1 – Quality-assessment tool for ChIP-seq data

SSP 1.2.1

:: DESCRIPTION

SSP (Strand-shift Profile) is a tool for quality assessment of ChIP-seq data without peak calling.

::DEVELOPER

Nakato lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux / MacOs
Gcc compilar

:: DOWNLOAD

SSP

:: MORE INFORMATION

Citation:

Nakato R, Shirahige K.
Sensitive and robust assessment of ChIP-seq read distribution using a strand-shift profile.
Bioinformatics. 2018 Jul 15;34(14):2356-2363. doi: 10.1093/bioinformatics/bty137. PMID: 29528371.

ArrayExpressHTS 1.42.0 – RNA-seq data Processing and Quality Assessment

ArrayExpressHTS 1.42.0

:: 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.

Admixem v1.0.2.2 – Quality Assessment Tool for Metagenome Assemblies

Admixem v1.0.2.2

:: 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.

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.

MASS – Protein Single-Model Global Quality Assessment by Random Forest and Various Energies

MASS

:: DESCRIPTION

MASS is a QA method to predict the global qualities of individual protein models using random forests and various novel energy functions.

::DEVELOPER

Z. WANG LAB

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Web browser

:: DOWNLOAD

:: MORE INFORMATION

Citation

Liu T, Wang Z.
MASS: predict the global qualities of individual protein models using random forests and novel statistical potentials.
BMC Bioinformatics. 2020 Jul 6;21(Suppl 4):246. doi: 10.1186/s12859-020-3383-3. PMID: 32631256; PMCID: PMC7336608.

TEQC 4.12.0 – Quality Assessment of Target Enrichment Experiments

TEQC 4.12.0

:: 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.

ATACseqQC 1.14.4 – Quality Assessment of ATAC-seq data

ATACseqQC 1.14.4

:: DESCRIPTION

ATACseqQC is a Bioconductor package for easily generating various diagnostic plots to help researchers quickly assess the quality of their ATAC-seq (Assays for Transposase-Accessible Chromatin using sequencing) data. In addition, this package contains functions to preprocess aligned ATAC-seq data for subsequent peak calling.

::DEVELOPER

Program in Gene Function and Expression@umassmed

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Windows/Linux/MacOsX
BioConductor
R package

:: DOWNLOAD

ATACseqQC

:: MORE INFORMATION

Citation:

Ou J, Liu H, Yu J, Kelliher MA, Castilla LH, Lawson ND, Zhu LJ.
ATACseqQC: a Bioconductor package for post-alignment quality assessment of ATAC-seq data.
BMC Genomics. 2018 Mar 1;19(1):169. doi: 10.1186/s12864-018-4559-3. PMID: 29490630; PMCID: PMC5831847.

SolexaQA 3.1.7.1 – Quality Assessment of Illumina Second-generation Sequencing data

SolexaQA 3.1.7.1

:: 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

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