Tag: Quality Control

NGS QC Toolkit v2.3.3 – Toolkit for the Quality Control (QC) of Next Generation Sequencing (NGS) data.

NGS QC Toolkit v2.3.3

:: DESCRIPTION

NGS QC Toolkit comprises of user-friendly stand alone tools for quality control of the sequence data generated using Illumina and Roche 454 platforms with detailed results in the form of tables and graphs, and filtering of high-quality sequence data. It also includes few other tools, which are helpful in NGS data quality control and analysis.

::DEVELOPER

Mukesh Jain (mjain@nipgr.ac.in); Ravi Patel (ravi_patel_4@yahoo.co.in) @ National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, India

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows/ MacOsX
  • Perl

:: DOWNLOAD

 NGS QC Toolkit

:: MORE INFORMATION

Citation

PLoS One. 2012;7(2):e30619. doi: 10.1371/journal.pone.0030619. Epub 2012 Feb 1.
NGS QC Toolkit: a toolkit for quality control of next generation sequencing data.
Patel RK1, Jain M.

scRNABatchQC v0.10.3 – multi-samples Quality Control for single cell RNA-seq data

scRNABatchQC v0.10.3

:: DESCRIPTION

scRNABatchQC is an R package for generating a HTML QC report to check and compare quality of multiple single cell RNA-seq datasets. scRNABatchQC supports multiple types of inputs, including gene-cell count matrices, 10x genomics, SingleCellExperiment or Seurat v3 objects.

::DEVELOPER

scRNABatchQC team

:: REQUIREMENTS

  • Linux
  • R

:: DOWNLOAD

scRNABatchQC

:: MORE INFORMATION

Citation

Liu Q, Sheng Q, Ping J, Ramirez MA, Lau KS, Coffey RJ, Shyr Y.
scRNABatchQC: multi-samples quality control for single cell RNA-seq data.
Bioinformatics. 2019 Dec 15;35(24):5306-5308. doi: 10.1093/bioinformatics/btz601. PMID: 31373345; PMCID: PMC6954654.

QCGWAS 1.0-8 – Quality Control of Genome Wide Association Study results

QCGWAS 1.0-8

:: DESCRIPTION

QCGWAS is an R package that automates the quality control of genome-wide association result files.

::DEVELOPER

Peter J. van der Most <p.j.van.der.most at umcg.nl> and Ilja M. Nolte

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux /Windows/ MacOsX
  • R

:: DOWNLOAD

 QCGWAS

:: MORE INFORMATION

Citation

Bioinformatics. 2014 Jan 13.
QCGWAS: A flexible R package for automated quality control of genome-wide association results.
van der Most PJ1, Vaez A, Prins BP, Munoz ML, Snieder H, Alizadeh BZ, Nolte IM.

EasyQC 23.8 – Quality Control of Genome-wide Association Meta-analyses

EasyQC 23.8

:: DESCRIPTION

EasyQC is an R-package that provides advanced funcionality

(i) to perform file-level QC of single genome-wide association (GWA) data-sets;

(ii) to conduct quality control across several GWA data-sets (meta-level QC);

(iii) to simplify data-handling of large-scale GWA data-sets

::DEVELOPER

The Genetic Epidemiology Unit

:: SCREENSHOTS

N/A

::REQUIREMENTS

  • Linux/Windows/MacOsX
  • R

:: DOWNLOAD

 EasyQC

:: MORE INFORMATION

Citation

Nat Protoc. 2014 May;9(5):1192-212. doi: 10.1038/nprot.2014.071. Epub 2014 Apr 24.
Quality control and conduct of genome-wide association meta-analyses.
Winkler et al.; Genetic Investigation of Anthropometric Traits (GIANT) Consortium.

RNA-SeQC 1.1.8 – Quality Control Metrics for RNA-seq data

RNA-SeQC 1.1.8

:: DESCRIPTION

RNA-SeQC is a java program which computes a series of quality control metrics for RNA-seq data

::DEVELOPER

The Cancer Genome Analysis (CGA) group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Mac OsX / Windows
  • Java 

:: DOWNLOAD

 RNA-SeQC

:: MORE INFORMATION

Citation

Deluca DS, Levin JZ, Sivachenko A, Fennell T, Nazaire MD, Williams C, Reich M, Winckler W, Getz G. (2012)
RNA-SeQC: RNA-seq metrics for quality control and process optimization.
Bioinformatics (2012) 28 (11): 1530-1532.

snpQC – Quality Control of Illumina SNP Genotyping Array data

snpQC

:: DESCRIPTION

snpQC is an R based fully automated pipeline for preprocessing, storage and quality control of Illumina SNP data.

::DEVELOPER

Cedric Gondro

:: SCREENSHOTS

n/a

:: REQUIREMENTS

  • Linux / MacOsX/ Windows
  • R

:: DOWNLOAD

  snpQC

:: MORE INFORMATION

Citation

Anim Genet. 2014 Oct;45(5):758-61. doi: 10.1111/age.12198. Epub 2014 Jul 18.
SNPQC–an R pipeline for quality control of Illumina SNP genotyping array data.
Gondro C1, Porto-Neto LR, Lee SH.

QuaCRS 1.2 – Quality Control for RNA-Seq

QuaCRS 1.2

:: DESCRIPTION

QuaCRS is an integrated, simplified quality control (QC) system for RNA-seq data that allows easy execution of several open-source QC tools, aggregation of their output, and the ability to quickly identify quality issues by performing meta-analyses on QC metrics across large numbers of samples in different studies.

:: DEVELOPER

QuaCRS team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Python

:: DOWNLOAD

 QuaCRS

:: MORE INFORMATION

Citation

Cancer Inform. 2014 Oct 15;13(Suppl 3):7-14. doi: 10.4137/CIN.S14022. eCollection 2014.
Quality Control for RNA-Seq (QuaCRS): An Integrated Quality Control Pipeline.
Kroll KW, Mokaram NE, Pelletier AR, Frankhouser DE, Westphal MS, Stump PA, Stump CL, Bundschuh R, Blachly JS, Yan P

Indexcov – Fast Coverage Quality Control for Whole-genome Sequencing

Indexcov

:: DESCRIPTION

Indexcov is an efficient estimator of whole-genome sequencing coverage to rapidly identify samples with aberrant coverage profiles, reveal large scale chromosomal anomalies, recognize potential batch effects, and infer the sex of a sample.

::DEVELOPER

The Quinlan Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • GO

:: DOWNLOAD

Indexcov

:: MORE INFORMATION

Citation:

Gigascience. 2017 Nov 1;6(11):1-6. doi: 10.1093/gigascience/gix090.
Indexcov: fast coverage quality control for whole-genome sequencing.
Pedersen BS1,2, Collins RL3,4,5, Talkowski ME3,6,4,5, Quinlan AR

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.