BSeQC 1.4 – Quality Control of Bisulfite Sequencing Experiments

BSeQC 1.4

:: DESCRIPTION

BSeQC is a quality control package specially for bisulfite sequencing experiments. It can comprehensively evaluate the quality of BS-seq experiments and automatically trim nucleotides with potential technical biases. In addition, BSeQC also support removing duplicate reads and keeping one copy of the overlapping segment in paired-end sequencing.

::DEVELOPER

Li Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Python

:: DOWNLOAD

 BSeQC

:: MORE INFORMATION

MethylAid 1.5.5 – Visual and interactive Quality Control of large Illumina 450k data sets

MethylAid 1.5.5

:: DESCRIPTION

MethylAid is specially designed for quality control of large sets of DNA methylation data e.g., epigenomewide association studies (EWAS).

::DEVELOPER

M. van Iterson <m.van_iterson at lumc.nl>

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows/ MacOsX
  • R
  • BioConductor

:: DOWNLOAD

 MethylAid

:: MORE INFORMATION

Citation

MethylAid: Visual and interactive quality control of large Illumina 450k data sets.
van Iterson M, Tobi EW, Slieker RC, den Hollander W, Luijk R, Slagboom PE, Heijmans BT.
Bioinformatics. 2014 Aug 21. pii: btu566.

FastQC 0.11.5 – Quality Control Tool for High Throughput Sequence Data

FastQC 0.11.5

:: DESCRIPTION

FastQC aims to provide a simple way to do some quality control checks on raw sequence data coming from high throughput sequencing pipelines. It provides a modular set of analyses which you can use to give a quick impression of whether your data has any problems of which you should be aware before doing any further analysis.

:: DEVELOPER

Babraham Bioinformatics

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux / Windows / MacOsX
  • Java 

:: DOWNLOAD

 FastQC

:: MORE INFORMATION

MRMPlusGUI 20151104 – Quality Control and Assessment tool for SRM/MRM Assay development

MRMPlusGUI 20151104

:: DESCRIPTION

MRMPlusGUI is a freely available, open-source tool in the platform independent Java programming language to compute analytical measures as recommended recently by the Clinical Proteomics Tumor Analysis Consortium Assay Development Working Group for “Tier 2” assays.

::DEVELOPER

MRMPlusGUI team

:: SCREENSHOTS

MRMPlus

:: REQUIREMENTS

  • MacOsX/Linux / Windows
  • Java

:: DOWNLOAD

 MRMPlusGUI

:: MORE INFORMATION

Citation

MRMPlus: an open source quality control and assessment tool for SRM/MRM assay development.
Aiyetan P, Thomas SN, Zhang Z, Zhang H.
BMC Bioinformatics. 2015 Dec 12;16(1):411. doi: 10.1186/s12859-015-0838-z.

GWAtoolbox 2.2.4-7 – Quality Control and Handling of Genome-wide Association Studies Meta-analysis data

GWAtoolbox 2.2.4-7

:: DESCRIPTION

GWAtoolbox is an R-package for fast quality control and data handling of multiple data files obtained from genome-wide association studies (GWAS).

::DEVELOPER

the Center of Biomedicine (CBM) at EURAC research.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/windows/MacOsX
  • R package

:: DOWNLOAD

 GWAtoolbox

:: MORE INFORMATION

Citation

Bioinformatics. 2012 Feb 1;28(3):444-5. doi: 10.1093/bioinformatics/btr679.
GWAtoolbox: an R package for fast quality control and handling of genome-wide association studies meta-analysis data.
Fuchsberger C, Taliun D, Pramstaller PP, Pattaro C; CKDGen consortium.

CloneStudio – Visualization for Synthetic Biology Quality Control

CloneStudio

:: DESCRIPTION

Synthetic biology projects require generation of error- free DNA molecules. A significant current bottleneck is assuring that DNA is error-free at the first point when it moves from an in vitro biochemical system to an in vivo cell-based host. CloneStudio helps eliminate this bottleneck by providing a visual interface to compare a desired sequence with sequence traces, basecalls for individual clones, and positions where the synthetic and desired sequences may differ.

::DEVELOPER

Joel Bader lab

:: SCREENSHOTS

CloneStudio

::REQUIREMENTS

  • Linux / Windows / MacOsX
  • JRE

:: DOWNLOAD

 CloneStudio

:: MORE INFORMATION

CloneQC – Quality Control on Sequenced Clones

CloneQC

:: DESCRIPTION

CloneQC is a public resource for lightweight sequence verification. The software pipeline is built from standard components, adapted for the purpose of validating relatively short synthetic DNA sequences easily checked in a single pair of reads from forward and reverse sequencing primers.

::DEVELOPER

Synthetic Biology Group (JHU)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

CLONEQC: lightweight sequence verification for synthetic biology.
Lee PA, Dymond JS, Scheifele LZ, Richardson SM, Foelber KJ, Boeke JD, Bader JS.
Nucleic Acids Res. 2010 May;38(8):2617-23. doi: 10.1093/nar/gkq093.

htSeqTools 1.16.0 – Quality Control, Visualization and Processing for High-Throughput Sequencing data

htSeqTools 1.16.0

:: DESCRIPTION

htSeqTools is a Bioconductor package with quality assessment, processing and visualization tools for high-throughput sequencing data, with emphasis in ChIP-seq and RNA-seq studies.

::DEVELOPER

Evarist Planet, Camille Stephan-Otto, Oscar Reina <oscar.reina at irbbarcelona.org>, Oscar Flores, David Rossell

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Mac OsX / Windows
  • R
  • Bioconductor

:: DOWNLOAD

 htSeqTools

:: MORE INFORMATION

Citation

htSeqTools: high-throughput sequencing quality control, processing and visualization in R.
Planet E, Attolini CS, Reina O, Flores O, Rossell D.
Bioinformatics. 2012 Feb 15;28(4):589-90. doi: 10.1093/bioinformatics/btr700.

RSeQC 2.6.2 – RNA-seq Quality Control package

RSeQC 2.6.2

:: DESCRIPTION

RSeQC package provides a number of useful modules that can comprehensively evaluate high throughput sequence data especially RNA-seq data. “Basic modules” quickly inspect sequence quality, nucleotide composition bias, PCR bias and GC bias, while “RNA-seq specific modules” investigate sequencing saturation status of both splicing junction detection and expression estimation, mapped reads clipping profile, mapped reads distribution, coverage uniformity over gene body, reproducibility, strand specificity and splice junction annotation

::DEVELOPER

Wei Li’s Computational Epigenomics Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/MacOsX
  • Python

:: DOWNLOAD

 RSeQC

:: MORE INFORMATION

Citation:

Bioinformatics. 2012 Aug 15;28(16):2184-5. doi: 10.1093/bioinformatics/bts356. Epub 2012 Jun 27.
RSeQC: quality control of RNA-seq experiments.
Wang L, Wang S, Li W.

caCORRECT 2.1 – Microarray Quality Control System

caCORRECT 2.1

:: DESCRIPTION

caCORRECT represents the next-generation of microarray quality control technology that fuses spatial artifact detection (similar to Harshlighting) and model-based techniques to provide improved gene expression data quality in the presence of artifacts.

::DEVELOPER

Bio-MIBLab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation:

BMC Bioinformatics. 2011 Sep 29;12:383. doi: 10.1186/1471-2105-12-383.
caCORRECT2: Improving the accuracy and reliability of microarray data in the presence of artifacts.
Moffitt RA1, Yin-Goen Q, Stokes TH, Parry RM, Torrance JH, Phan JH, Young AN, Wang MD.