NGS-QC Generator
A computational-based approach that infers quality indicators from the…
A computational-based approach that infers quality indicators from the distribution of sequenced reads associated to a particular NGS profile.
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Read quality control software tools | Whole-genome sequencing data analysis
Next-generation sequencing (NGS) technologies have been widely used in life sciences. However, several kinds of sequencing artifacts, including low-quality reads and contaminating reads, were found to be quite common in raw sequencing data, which…
Next-generation sequencing (NGS) technologies have been widely used in life sciences. However, several kinds of sequencing artifacts, including low-quality reads and contaminating reads, were found to be quite common in raw sequencing data, which compromise downstream analysis. Therefore, quality control (QC) is essential for raw NGS data.
Source text:
(Zhou et al., 2013) QC-Chain: fast and holistic quality control method for next-generation sequencing data. PLoS One.
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Trim Galore!
Trim Galore!
A wrapper tool around Cutadapt and FastQC to consistently apply quality and…
A wrapper tool around Cutadapt and FastQC to consistently apply quality and adapter trimming to FastQ files, with some extra functionality for MspI-digested RRBS-type (Reduced Representation…
ShortRead
ShortRead
A package for input, quality assessment, manipulation and output of…
A package for input, quality assessment, manipulation and output of high-throughput sequencing data. ShortRead extends Bioconductor with tools useful in the initial stages of short-read DNA sequence…
oneChannelGUI
oneChannelGUI
Facilitates analysis of microarrays and miRNA/RNA-seq data on laptops.…
Facilitates analysis of microarrays and miRNA/RNA-seq data on laptops. oneChannelGUI can be used for quality control, normalization, filtering, statistical validation and data mining for single…
aRNApipe
aRNApipe automated RNA-seq pipeline
Provides an integrated and efficient workflow for analyzing single-end and…
Provides an integrated and efficient workflow for analyzing single-end and stranded or unstranded paired-end RNA-seq data. Unlike previous pipelines, aRNApipe is focused on high performance computing…
NGS QC Toolkit
NGS QC Toolkit
A toolkit for the quality control (QC) of next generation sequencing (NGS)…
A toolkit for the quality control (QC) of next generation sequencing (NGS) data. The toolkit comprises of user-friendly standalone tools for quality control of the sequence data generated using…
SAPAS
SAPAS
A pipeline for RNA-seq method to research polyA. SAPAS performs a systematic…
A pipeline for RNA-seq method to research polyA. SAPAS performs a systematic search and evaluation of protocols for typical steps to investigate to what extent these can indeed facilitate RNA-seq…
RseqFlow
RseqFlow
An RNA-Seq analysis pipeline which offers an express implementation of analysis…
An RNA-Seq analysis pipeline which offers an express implementation of analysis steps for RNA sequencing datasets.
SolexaQA
SolexaQA
A user-friendly software package designed to generate detailed statistics and…
A user-friendly software package designed to generate detailed statistics and at-a-glance graphics of sequence data quality both quickly and in an automated fashion. SolexaQA contains associated…
S-MART
S-MART
A toolkit for RNA-Seq analysis. S-MART performs two categories of tasks : data…
A toolkit for RNA-Seq analysis. S-MART performs two categories of tasks : data manipulation and visualization. Manipulations include (i) selection/exclusion of the reads which overlap with some…
SAMStat
SAMStat
Displays statistics of large sequence files from next-generation sequencing…
Displays statistics of large sequence files from next-generation sequencing (NGS) projects. SAMStat is a program which plots nucleotide over-representation and other statistics in mapped and unmapped…
FQC
FQC
Facilitates quality control (QC) of FASTQ files. FQC combines a command line…
Facilitates quality control (QC) of FASTQ files. FQC combines a command line interface (CLI) depending on FastQC for processing FASTQ files, and a frontend website for plotting, styling and…
Pheniqs
Pheniqs PHilology ENcoder wIth Quality Statistics
Demultiplexes sequence and analyzes quality. Pheniqs introduces a…
Demultiplexes sequence and analyzes quality. Pheniqs introduces a Phred-adjusted maximum likelihood decoder that consults base calling quality scores and estimates the probability of a barcode…
ST Pipeline
ST Pipeline
Permits to process and analyze the raw files generated with the Spatial…
Permits to process and analyze the raw files generated with the Spatial Transcriptomics (ST) method. ST Pipeline enables demultiplexing of spatially-resolved RNA-seq data and robust quality filtering…
NGSCheckMate
NGSCheckMate
Verifies sample identities from FASTQ, BAM or VCF files. NGSCheckMate uses a…
Verifies sample identities from FASTQ, BAM or VCF files. NGSCheckMate uses a model-based method to compare allele read fractions at known single-nucleotide polymorphisms (SNPs), considering…
ClinQC
ClinQC
An integrated, automated, flexible and user-friendly tool for quality control…
An integrated, automated, flexible and user-friendly tool for quality control in clinical research. It supports three major NGS sequencing technologies including Illumina, 454 and Ion Torrent along…
TRAPLINE
TRAPLINE Transparent Reproducible and Automated PipeLINE
Integrates the best performing data analysis, data evaluation and annotation…
Integrates the best performing data analysis, data evaluation and annotation methods in a Transparent, Reproducible and Automated PipeLINE for RNA sequencing data processing (suitable for Illumina,…
SePIA
SePIA Sequence Processing Integration and Analysis
An open-source workflow introducing standardized processing and analysis of RNA…
An open-source workflow introducing standardized processing and analysis of RNA and small RNA data. SePIA provides ready execution for over 20 commonly known RNA-seq tools on top of an established…
wapRNA
wapRNA
This is a free web-based application for the processing of high-throughput…
This is a free web-based application for the processing of high-throughput RNA-Seq data from next generation sequencing (NGS) platforms, such as Genome Analyzer of Illumina Inc. (Solexa) and SOLiD of…
MuffinInfo
MuffinInfo
A FastQ/Fasta/SAM information extractor implemented in HTML5 capable of…
A FastQ/Fasta/SAM information extractor implemented in HTML5 capable of offering insights into next-generation sequencing (NGS) data. MuffinInfo can run on any software or hardware environment, in…
Kraken
Kraken
A set of tools for quality control and analysis of high-throughput sequence…
A set of tools for quality control and analysis of high-throughput sequence data.
Zika-RNAseq-Pip…
Zika-RNAseq-Pipeline
Provides an open source RNA-seq processing pipeline that can be used to extract…
Provides an open source RNA-seq processing pipeline that can be used to extract knowledge from any study that profiled gene expression using RNA-seq applied to mammalian cells, comparing two…
MetaTrans
MetaTrans
Analyzes the structure and functions of active microbial communities using the…
Analyzes the structure and functions of active microbial communities using the power of multi-threading computers. MetaTrans is designed to perform two types of RNA-Seq analyses: taxonomic and gene…
miARma-Seq
miARma-Seq
Designed for mRNA, miRNA and circRNA identification and differential expression…
Designed for mRNA, miRNA and circRNA identification and differential expression analysis, applicable to any sequenced organism. miARma-Seq is presented as a stand-alone tool that provides different…
KAT
KAT K-mer Analysis Toolkit
A user-friendly, extendible and scalable toolkit for rapidly counting,…
A user-friendly, extendible and scalable toolkit for rapidly counting, comparing and analysing k-mers from various data sources. The tools in KAT assist the user with a wide range of tasks including…
MultiQC
MultiQC
A tool to create a single report visualizing output from multiple tools across…
A tool to create a single report visualizing output from multiple tools across many samples, enabling global trends and biases to be quickly identified. MultiQC allows accurate comparison between…
AlmostSignifica…
AlmostSignificant
An open-source platform for aggregating multiple sources of quality metrics as…
An open-source platform for aggregating multiple sources of quality metrics as well as meta-data associated with DNA sequencing runs from Illumina NextSeq and HiSeq machines. AlmostSignificant is a…
HTQC
HTQC High-Throughput Quality Control
A toolkit named for sequence reads quality control, which consists of six…
A toolkit named for sequence reads quality control, which consists of six programs for reads quality assessment, reads filtration and generation of graphic reports. The HTQC toolkit can generate…
NGSQC
NGSQC Next Generation Sequencing Quality Control
Provides a set of quality control measures to detect quality issues in deep…
Provides a set of quality control measures to detect quality issues in deep sequencing data derived from 2D surfaces. NGSQC is a comprehensive deep sequencing quality control pipeline that can help…
QUASR
QUASR Quality Assessment of Short Read
A lightweight pipeline written to process and analyse next-generation…
A lightweight pipeline written to process and analyse next-generation sequencing (NGS) data from Illumina, 454, and Ion Torrent platforms.
RNA-seq portal
RNA-seq portal
Offers three integrated workflows to perform computing and analysis, including…
Offers three integrated workflows to perform computing and analysis, including sequence quality control, read-mapping, transcriptome assembly, reconstruction and differential analysis. The first…
SUGAR
SUGAR SUbtile-based GUI-Assisted Refiner
Enables rapid evaluation and cleaning of the Illumina HiSeq and MiSeq data,…
Enables rapid evaluation and cleaning of the Illumina HiSeq and MiSeq data, specifically considering technical errors in flowcells and sequencing run.
countsimQC
countsimQC
Allows user to explore and compare a variety of characteristics across one or…
Allows user to explore and compare a variety of characteristics across one or more count data sets. countsimQC can generate a summary report for evaluation and dissemination. User can visualize the…
Hercules
Hercules
Detects possible sources of sequence-specific bias in short read data. Hercules…
Detects possible sources of sequence-specific bias in short read data. Hercules is based on analyzing sequence motif correlations and employs the MapReduce formalism of Apache Spark to quantify bias…
AfterQC
AfterQC
Processes FASTQ files in batches. AfterQC is an application with rich quality…
Processes FASTQ files in batches. AfterQC is an application with rich quality control, data filtering, error profiling and correction functions for next generation sequencing (NGS) data. This method…
NGS-pipe
NGS-pipe
Allows to develop tailored workflows for the analysis of whole-exome (WES),…
Allows to develop tailored workflows for the analysis of whole-exome (WES), whole-genome (WGS), and transcriptome (RNA-seq) sequencing data. NGS-pipe is an automated framework for the design of…
NGS-Bits
NGS-Bits
Permits quality control of Next-Generation-Sequencing (NGS) tumor-normal…
Permits quality control of Next-Generation-Sequencing (NGS) tumor-normal experiments. NGS-Bits is separate into four steps: (1) gather information from raw reads, (2) map reads, (3) extract variant…
zUMIs
zUMIs
Processes raw reads to count tables for RNA-seq data using Unique Molecular…
Processes raw reads to count tables for RNA-seq data using Unique Molecular Identifiers (UMIs). zUMIs is a pipeline applicable for most experimental designs of RNA-seq data, such as single-nuclei…
RNA workbench
RNA workbench
Establishes a central, redistributable workbench for scientists and programmers…
Establishes a central, redistributable workbench for scientists and programmers working with RNA-related data. The RNA workbench builds a sustainable community around it. This platform is unique in…
Zseq
Zseq
Identifies the most informative genomic sequences and reduces the number of…
Identifies the most informative genomic sequences and reduces the number of biased sequences, sequence duplications, and ambiguous nucleotides. Zseq is a linear method that finds the complexity of…
QASDRA
QASDRA Quality Assessment of Sequencing Data via Range Analysis
Detects ranges and introduces new metrics computed from their lengths. QASDRA…
Detects ranges and introduces new metrics computed from their lengths. QASDRA creates the quality assessment report of an input FASTQ file according to the user specified k and v parameters. The…
AEHTS
AEHTS ArrayExpressHTS
A package that allows the users to obtain a standard Bioconductor ExpressionSet…
A package that allows the users to obtain a standard Bioconductor ExpressionSet object containing expression levels from raw sequence files with a single R function call. ArrayExpressHTS is an…
RNA-Rocket
RNA-Rocket
A free service that provides access to RNA-Seq and ChIP-Seq analysis tools for…
A free service that provides access to RNA-Seq and ChIP-Seq analysis tools for studying infectious diseases. The site makes available thousands of pre-indexed genomes, their annotations, and the…
HTSeq
HTSeq
A Python library to facilitate the rapid development of scripts. HTSeq offers…
A Python library to facilitate the rapid development of scripts. HTSeq offers parsers for many common data formats in HTS projects, as well as classes to represent data, such as genomic coordinates,…
Pyrocleaner
Pyrocleaner
It is intended to clean the reads included in the sff file in order to ease the…
It is intended to clean the reads included in the sff file in order to ease the assembly process.
QuickNGS
QuickNGS
A workflow system for laboratories with the need to analyze data from multiple…
A workflow system for laboratories with the need to analyze data from multiple NGS projects at a time. QuickNGS takes advantage of parallel computing resources, a comprehensive back-end database, and…
RAP
RAP RNA-seq Analysis Pipeline
A cloud computing web application implementing a complete but modular analysis…
A cloud computing web application implementing a complete but modular analysis workflow. This pipeline integrates both state-of-the-art bioinformatics tools for RNA-Seq analysis and in-house…
Glbase
Glbase
Allows the user to perform many common analyses on ChIP-seq, microarray and…
Allows the user to perform many common analyses on ChIP-seq, microarray and RNA-seq data. Glbase is a flexible and multifunctional toolkit which includes many functions to intersect two lists of…
RNA-QC-Chain
RNA-QC-Chain
A comprehensive and fast quality control for RNA-Seq data. RNAQC-Chain can…
A comprehensive and fast quality control for RNA-Seq data. RNAQC-Chain can accomplish the data QC on three levels: (i) sequencing-quality assessment and trimming; (ii) detection and filtration of…
poretools
poretools
A flexible toolkit for exploring datasets generated by nanopore sequencing…
A flexible toolkit for exploring datasets generated by nanopore sequencing devices from MinION for the purposes of quality control and downstream analysis. Poretools operates directly on the native…
OncoRep
OncoRep Oncogenomics Report
A fully automated RNA-Seq based report for patients with (breast) cancer, which…
A fully automated RNA-Seq based report for patients with (breast) cancer, which includes molecular classification, detection of altered genes, detection of altered pathways, identification of gene…
BIGpre
BIGpre
A quality assessment package for next-genomics sequencing data. BIGpre contains…
A quality assessment package for next-genomics sequencing data. BIGpre contains all the functions of other quality assessment software, such as the correlation between forward and reverse reads, read…
Rqc
Rqc
Allows quality control and assessment of high-throughput sequencing data. Rqc…
Allows quality control and assessment of high-throughput sequencing data. Rqc performs parallel processing of entire files and produces a report which contains a set of high-resolution graphics. It…
savR
savR
Parses Illumina Sequence Analysis Viewer (SAV) files, access data, and generate…
Parses Illumina Sequence Analysis Viewer (SAV) files, access data, and generate QC plots. SavR offers functions to generate a folder of images that approximates the format of the folder that was…
FastQt
FastQt
Provides a quality control tool for high throughput sequence data. FastQt is…
Provides a quality control tool for high throughput sequence data. FastQt is the clone of FastQC application ported from Java to C++/Qt5. FastQt aims to provide a simple way to do some quality…
StatsDB
StatsDB
An open-source software package for storage and analysis of next generation…
An open-source software package for storage and analysis of next generation sequencing run metrics. StatsDB has been designed for incorporation into a primary analysis pipeline, either at the…
poreminion
poreminion
Additional tools for analyzing Oxford Nanopore minION data. poreminion contains…
Additional tools for analyzing Oxford Nanopore minION data. poreminion contains some tools that have been made on top of Aaron R. Quinlan's and Nicholas J. Loman's poretools, and therefore…
CLC Genomics…
CLC Genomics Workbench
Allows to analyze, compare, and visualize next generation sequencing (NGS)…
Allows to analyze, compare, and visualize next generation sequencing (NGS) data. CLC Genomics Workbench offers a complete and customizable solution for genomics, transcriptomics, epigenomics, and…
qrqc
qrqc Quick Read Quality Control
Quickly scans reads and gathers statistics on base and quality frequencies,…
Quickly scans reads and gathers statistics on base and quality frequencies, read length, and frequent sequences.
Picard
Picard
A set of tools (in Java) for working with next generation sequencing data in…
A set of tools (in Java) for working with next generation sequencing data in the BAM format.
mubiomics
mubiomics
A set of scripts (mostly python) for processing reads generated by the Roche…
A set of scripts (mostly python) for processing reads generated by the Roche 454 or Illumina next-gen sequencing platforms.
subN
subN
Masks substitutes low quality base calls with ‘N’s (undetermined bases) in…
Masks substitutes low quality base calls with ‘N’s (undetermined bases) in Next generation sequencing (NGS) data. subN is an effective preprocessing method for NGS data analysis since masking…
FaQCs
FaQCs FastQ Quality Control Software
A software package that can rapidly process large volumes of data, and which…
A software package that can rapidly process large volumes of data, and which improves upon previous solutions to monitor the quality and remove poor quality data from sequencing runs. FaQCs combines…
SeqAssist
SeqAssist
Takes NGS-generated FASTQ files as the input, employs the BWA-MEM aligner for…
Takes NGS-generated FASTQ files as the input, employs the BWA-MEM aligner for sequence alignment, and aims to provide a quick overview and basic statistics of NGS data. SeqAssist is a useful and…
NG6
NG6
A user-friendly information system able to manage large sets of sequencing…
A user-friendly information system able to manage large sets of sequencing data. It includes, a workflow environment already containing pipelines adapted to different input formats, different…
PathoQC
PathoQC
Pre-processes next-generation sequencing (NGS) data. PathoQC is based on…
Pre-processes next-generation sequencing (NGS) data. PathoQC is based on several of the most used quality control software approaches and combines their benefits to offer a variety of quality control…
QuaCRS
QuaCRS Quality Control for RNA-Seq
An integrated, simplified quality control (QC) system for RNA-seq data that…
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…
QCumber
QCumber
Aims to explore next-generation sequencing (NGS) data. QCumber allows user to…
Aims to explore next-generation sequencing (NGS) data. QCumber allows user to work about quality control, to extract data from sequence analysis viewer, or to classify reads.
fastq.bio
fastq.bio
Allows quality control of DNA sequencing data. fastq.bio offers an interactive…
Allows quality control of DNA sequencing data. fastq.bio offers an interactive and easy-to-use interface.
basecallQC
basecallQC
Provides package to work with Illumina bcl2Fastq software. basecallQC functions…
Provides package to work with Illumina bcl2Fastq software. basecallQC functions allow the user to update Illumina sample sheets, clean sample sheets of common problems such as invalid sample names…
Partek Flow
Partek Flow
Enable researchers to self-sufficiently perform data analysis. Partek Flow…
Enable researchers to self-sufficiently perform data analysis. Partek Flow software is designed specifically for the analysis needs of next generation sequencing (NGS) applications including RNA,…
AIR
AIR Artificial intelligence RNAseq
Offers a solution to close the gap between data production and data…
Offers a solution to close the gap between data production and data interpretation, making it possible for researchers to do their own analysis in the simplest possible way and giving them the…
omnomicsQ
omnomicsQ
Supports clinical labs with fast, simple and visual quality control of next…
Supports clinical labs with fast, simple and visual quality control of next generation sequencing bioinformatics data. omnomicsQ is developed to provide an objective, third party evaluation based on…
QRNAseq
QRNAseq
A tool to manage huge amounts of RNA-seq data in an integrative way which…
A tool to manage huge amounts of RNA-seq data in an integrative way which includes RNA-seq data quality control, read alignment, gene fusion, gene mutation, isoform identification and function…
stsPlots
stsPlots
Plot primary analysis quality control metrics to assess potential SMRTcell…
Plot primary analysis quality control metrics to assess potential SMRTcell loading problems.
Illuminate
Illuminate
Python module and utilities to parse the metrics binaries output by Illumina…
Python module and utilities to parse the metrics binaries output by Illumina sequencers.
bcbio-nextgen
bcbio-nextgen
A python toolkit providing best-practice pipelines for fully automated high…
A python toolkit providing best-practice pipelines for fully automated high throughput sequencing analysis. You write a high level configuration file specifying your inputs and analysis parameters.…
NGS-TOOLBOX
NGS-TOOLBOX
This collection of simple Perl scripts is adressed to scientists doing research…
This collection of simple Perl scripts is adressed to scientists doing research that bases on high throughput genomic/transcriptomic data.
CorQ
CorQ
Quality score based identification and correction of pyrosequencing errors.
Quality score based identification and correction of pyrosequencing errors.
FastQ Screen
FastQ Screen
Allows you to screen a library of sequences in FastQ format against a set of…
Allows you to screen a library of sequences in FastQ format against a set of sequence databases so you can see if the composition of the library matches with what you expect.
FastQC
FastQC
A quality control tool for high throughput sequence data. FastQC aims to…
A quality control tool for high throughput sequence data. FastQC aims to provide a simple way to do some quality control checks on raw sequence data coming from high throughput sequencing pipelines.…
FASTX-Toolkit
FASTX-Toolkit
A collection of command line tools for Short-Reads FASTA/FASTQ files…
A collection of command line tools for Short-Reads FASTA/FASTQ files preprocessing. Next-Generation sequencing machines usually produce FASTA or FASTQ files, containing multiple short-reads sequences…
Array Studio
Array Studio
Provides the premier enterprise solution for data content, framework and…
Provides the premier enterprise solution for data content, framework and graphical user interface for omic and next-generation sequencing data analysis. Array Suite (Array Studio and Array Server)…
RobiNA
RobiNA
A User Friendly Graphical Interface to Powerful Open Source Microarray and…
A User Friendly Graphical Interface to Powerful Open Source Microarray and RNA-Seq Processing.
PIQA
PIQA
A quality analysis pipeline designed to examine genomic reads produced by Next…
A quality analysis pipeline designed to examine genomic reads produced by Next Generation Sequencing technology (Illumina G1 Genome Analyzer). A short statistical summary, as well as tile-by-tile and…
QC-Chain
QC-Chain
A fast, accurate and holistic NGS data quality-control method. The tool…
A fast, accurate and holistic NGS data quality-control method. The tool synergeticly comprised of user-friendly tools for (1) quality assessment and trimming of raw reads using Parallel-QC, a fast…
