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.

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

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.

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.

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 , Ira Hall 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

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.

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.