Tag: Quality Control

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

Parallel-QC 1.0 – A Parallel Quality Control computational engine for NGS data

Parallel-QC 1.0

:: DESCRIPTION

Parallel-QC is a fast computational engine specifically designed for general NGS data QC. Parallel-QC can complete sequencing-quality assessment accuracy and efficiency. Possible contaminating species could also be identified without any prior information. And the whole processing of Parallel-QC is quite fast since it is optimized based on parallel computation.

::DEVELOPER

Bioinformatics Group , Single-cell Reseearch Center of Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences (QIBEBT-CAS).

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • C Compiler

:: DOWNLOAD

 Parallel-QC

:: MORE INFORMATION

Citation

PLoS One. 2013;8(4):e60234. doi: 10.1371/journal.pone.0060234. Epub 2013 Apr 2.
QC-Chain: fast and holistic quality control method for next-generation sequencing data.
Zhou Q1, Su X, Wang A, Xu J, Ning K.

htSeqTools 1.31.0 – Quality Control, Visualization and Processing for High-Throughput Sequencing data

htSeqTools 1.31.0

:: 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.

MetaQC 0.1.13 – Quality Control and Diagnosis for Microarray Meta-analysis

MetaQC 0.1.13

:: DESCRIPTION

MetaQC: A diagnosis tool for assessing quality of genomic studies for meta-analysis and determining inclusion/exclusion criteria.

::DEVELOPER

George C. Tseng 

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 MetaQC

:: MORE INFORMATION

Citation

Dongwan D. Kang, Etienne Sibille, Naftali Kaminski, and George C. Tseng*. (2011)
MetaQC: Objective Quality Control and Inclusion/Exclusion Criteria for Genomic Meta-Analysis.
Nucl. Acids Res. (2011) doi: 10.1093/nar/gkr1071

AffyGCQC 1.02 – GeneChip Data Quality Control

AffyGCQC 1.02

:: DESCRIPTION

AffyGCQC is the acronym for a bioinformatics tool designed to perform Affymetrix GeneChip Quality Control. This program implements a graphical representation of QC metrics recommended by Affymetrix for GeneChip oligonucleotide array technology. Most importantly, it performs extreme studentized deviate statistical tests for the set of arrays being compared in a given experiment, thus providing an objective measure for outlier detection.

DEVELOPER

Osorio Y Fortéa J, Prina E, Lang T, Milon G, Davory C, Coppée JY, Regnault B.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux / MacOsX
  • Apache
  • R Package
  • Perl

:: DOWNLOAD

 AffyGCQC

:: MORE INFORMATION

Citation

J Bioinform Comput Biol. 2008 Apr;6(2):317-34.
AffyGCQC: a web-based interface to detect outlying genechips with extreme studentized deviate tests.
Osorio Y Fortéa J, Prina E, Lang T, Milon G, Davory C, Coppée JY, Regnault B.

SAQC 1.0 – SNP Array Quality Control

SAQC 1.0

:: DESCRIPTION

SAQC (SNP Array Quality Control)software is written in R and R-GUI and was developed as a user-friendly tool for the visualization and evaluation of data quality of genome-wide SNP arrays.

::DEVELOPER

Hsin-Chou Yang

:: SCREENSHOTS

::REQUIREMENTS

:: DOWNLOAD

 SAQC

:: MORE INFORMATION

Citation

Hsin-Chou Yang*, Hsin-Chi Lin, Meijyh Kang, Chun-Houh Chen, Chien-Wei Lin, Ling-Hui Li, Jer-Yuarn Wu, Yuan-Tsong Chen, and Wen-Harn Pan (2011).
SAQC: SNP array quality control.
BMC Bioinformatics 12, 100.