Tag: Quality Control

QCTOOL 2.0.8 – SNP Quality Control (QC) for Genome-wide Association Studies

QCTOOL 2.0.8

:: DESCRIPTION

QCTOOL is a command-line utility program for basic quality control of gwas datasets. It supports the same file formats used by the WTCCC studies, as well as the binary file format described here, and is designed to work seamlessly with SNPTEST and related tools. QCTOOL computes per-sample and per-SNP summary statistics, and uses these to filter out samples and SNPs from the dataset (either by removing them from the files or by writing exclusion lists).

::DEVELOPER

Gavin Band , Jonathan Marchini 

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • MacOsX /  Linux

:: DOWNLOAD

 QCTOOL

:: MORE INFORMATION

MethylAid 1.27.0 – Visual and interactive Quality Control of large Illumina 450k data sets

MethylAid 1.27.0

:: 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.

AgileQualityFilter 20121127 – Quality Control, Detagging and Reformatting of Clonal Sequencing data

AgileQualityFilter 20121127

:: DESCRIPTION

AgileQualityFilter performs a number of pre-alignment tasks on sequence data from an Illumina GA-II clonal sequencer. The primary function of AgileQualityFilter is to remove low quality sequence data before alignment to a reference sequence.

::DEVELOPER

Ian’s DNA@Leeds

:: SCREENSHOTS

AgileQualityFilter

:: REQUIREMENTS

  • Windows
  • Microsoft .NET framework version 2.0 

:: DOWNLOAD

 AgileQualityFilter

:: MORE INFORMATION

FastQC 0.11.9 – Quality Control Tool for High Throughput Sequence Data

FastQC 0.11.9

:: 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

HumMeth27QCReport 1.2.14 – Quality Control of Illumina’s Infinium BeadChip Methylation Assays

HumMeth27QCReport 1.2.14

:: DESCRIPTION

HumMeth27QCReport is an R package that permits a quick overview of the quality of Illumina’s Infinium BeadChip methylation assays.

::DEVELOPER

Bioinformatics Core @ CRG

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ MacOsX/Windows
  • R package
  • perl

:: DOWNLOAD

 HumMeth27QCReport

:: MORE INFORMATION

Citation

BMC Res Notes. 2011 Dec 19;4:546. doi: 10.1186/1756-0500-4-546.
HumMeth27QCReport: an R package for quality control and primary analysis of Illumina Infinium methylation data.
Mancuso FM, Montfort M, Carreras A, Alibés A, Roma G.

MASQOT-GUI 1.0.1 – Two-channel Microarray Spot Quality Control

MASQOT-GUI 1.0.1

:: DESCRIPTION

MASQOT-GUI provides an open-source, platform-independent software pipeline for two-channel microarray spot quality control. This includes gridding, segmentation, quantification, quality assessment and data visualization. It hosts three independent applications (MASQOTGrid, MASQOTSeg and MASQOTView) for this purpose with interactions between the tools as well as import and export support for external software.

::DEVELOPER

MASQOT-GUI team

:: SCREENSHOTS

MASQOT-GUI

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • Java

:: DOWNLOAD

 MASQOT-GUI

:: MORE INFORMATION

Citation

Bioinformatics. 2006 Oct 15;22(20):2554-5. Epub 2006 Aug 9.
MASQOT-GUI: spot quality assessment for the two-channel microarray platform.
Bylesjö M1, Sjödin A, Eriksson D, Antti H, Moritz T, Jansson S, Trygg J.

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.

Kraken 13-274 – Tools for Quality Control and Analysis of High-throughput Sequence data

Kraken 13-274

:: DESCRIPTION

Kraken consists of 3 tools ( Reaper ,  Tally  and  Sequence Imp ) designed to streamline the analysis of next-generation sequencing data. Although designed with small RNA sequence analysis in mind the tools can be used to address issues facing next-generation sequencing in general.

::DEVELOPER

Enright Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • MacOsX /  Linux

:: DOWNLOAD

 Kraken

:: MORE INFORMATION

Citation:

Kraken: A set of tools for quality control and analysis of high-throughput sequence data
Matthew P.A. Davis, Stijn van Dongen, Cei Abreu-Goodger, Nenad Bartonicek and Anton J. Enright
Methods. 2013 Sep 1;63(1):41-9. doi: 10.1016/j.ymeth.2013.06.027. Epub 2013 Jun 29.

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

Citation

Bioinformatics, 29 (24), 3227-9 2013 Dec 15
BSeQC: Quality Control of Bisulfite Sequencing Experiments
Xueqiu Lin , Deqiang Sun, Benjamin Rodriguez, Qian Zhao, Hanfei Sun, Yong Zhang, Wei Li

RSeQC v3.0.1 – RNA-seq Quality Control package

RSeQC v3.0.1

:: 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

Li 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.