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Alignment evaluation software tools | RNA sequencing data analysis

Accurate mapping of next-generation sequencing (NGS) reads to reference genomes is crucial for almost all NGS applications and downstream analyses. Various repetitive elements in human and other higher eukaryotic genomes contribute in large part to…
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AlignerBoost
Desktop

AlignerBoost

Estimates mapping quality of ambiguously mapped next generation sequencing…

Estimates mapping quality of ambiguously mapped next generation sequencing (NGS) reads. AlignerBoost utilizes a Bayesian-based framework, and tests with both simulated and real DNA-seq and RNA-seq…

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CLC Genomics…
Desktop

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…

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QualiMap
Desktop

QualiMap

A Java application that supports user-friendly quality control of mapping data,…

A Java application that supports user-friendly quality control of mapping data, by considering sequence features and their genomic properties. Qualimap takes sequence alignment data and provides…

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SeqControl
Desktop

SeqControl

A set of Perl and R scripts designed to assess the quality of sequencing data…

A set of Perl and R scripts designed to assess the quality of sequencing data using multiple quality metrics. The pipeline takes one or more sorted BAM files as input, and outputs multiple files…

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RSeQC
Desktop

RSeQC

Evaluates different aspects of RNA-seq experiments, such as sequence quality,…

Evaluates different aspects of RNA-seq experiments, such as sequence quality, GC bias, polymerase chain reaction bias, nucleotide composition bias, sequencing depth, strand specificity, coverage…

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QuickRNASeq
Desktop

QuickRNASeq

Advances the automation and visualization of RNA-seq data analyses results.…

Advances the automation and visualization of RNA-seq data analyses results. QuickRNASeq is a pipeline that significantly reduces data analysts’ hands-on time, which results in a substantial…

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seqbias
Desktop

seqbias

Estimation of per-position bias in high-throughput sequencing data. This…

Estimation of per-position bias in high-throughput sequencing data. This package implements a model of per-position sequencing bias in high-throughput sequencing data using a simple Bayesian network,…

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RNA-SeQC
Desktop

RNA-SeQC

A java program which computes a series of quality control metrics for RNA-seq…

A java program which computes a series of quality control metrics for RNA-seq data.

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RseqFlow
Desktop

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.

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NGSCheckMate
Desktop

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…

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QuasR
Desktop

QuasR

Provides an integrated analysis of high-throughput sequencing data in R,…

Provides an integrated analysis of high-throughput sequencing data in R, covering all steps from read preprocessing, alignment and quality control to quantification. QuasR supports different…

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dupRadar
Desktop

dupRadar

Offers straight-forward methods to assess RNA-seq datasets for problems with…

Offers straight-forward methods to assess RNA-seq datasets for problems with duplicate reads and is aimed towards simple integration into standard analysis pipelines as a default quality control…

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Teaser
Desktop
Web

Teaser

An analytical framework for benchmarking NGS read mappers. Teaser allows…

An analytical framework for benchmarking NGS read mappers. Teaser allows researchers to identify the optimal mapper, parameter set and mapping quality thresholds for data sets that mimic their real…

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MuffinInfo
Web
Desktop

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…

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BlackOPs
Desktop

BlackOPs

This page contains the necessary software to characterize mappability of…

This page contains the necessary software to characterize mappability of RNA-Seq reads and create a "blacklist" of genomic positions of mismapped reads.

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MultiQC
Desktop

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…

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ARDEN
Desktop

ARDEN Artificial Reference Driven Estimation of false positives in NGS data

A benchmark that estimates error rates based on real experimental reads and an…

A benchmark that estimates error rates based on real experimental reads and an additionally generated artificial reference genome. ARDEN allows the computation of error rates specifically for a…

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QoRTs
Desktop

QoRTs Quality of RNA-Seq Toolset

Produces a broad array of quality control metrics. QoRTs allows visualization…

Produces a broad array of quality control metrics. QoRTs allows visualization and comparison of RNA-seq data across numerous replicates sorted and differentiated by batch, biological condition,…

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deepTools
Desktop
Web

deepTools

A Galaxy based web server for processing and visualizing deeply sequenced data.…

A Galaxy based web server for processing and visualizing deeply sequenced data. The web server's core functionality consists of a suite of newly developed tools, called deepTools, that enable…

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ANAQUIN
Desktop

ANAQUIN

Facilitates the analysis of spike-in controls for next generation sequencing…

Facilitates the analysis of spike-in controls for next generation sequencing (NGS). ANAQUIN offers a way for users to evaluate the performance of spike-in controls and the accompanying RNA/DNA…

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NGS-Bits
Desktop

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…

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RNAseqEval
Desktop

RNAseqEval

Evaluates RNA-seq alignment results. RNAseqEval is a package that can be used…

Evaluates RNA-seq alignment results. RNAseqEval is a package that can be used to compare the alignment of simulated reads to their genomic origin, or to compare the alignment of real reads to a set…

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CADBURE
Desktop
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AEHTS
Desktop

AEHTS ArrayExpressHTS

Gives a standard Bioconductor ExpressionSet object containing expression levels…

Gives a standard Bioconductor ExpressionSet object containing expression levels from raw sequence files with a single R function call. ArrayExpressHTS allows pre-processing, expression estimation and…

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HTSeq
Desktop

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,…

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GeneScissors
Desktop

GeneScissors

A comprehensive approach to detecting and correcting spurious transcriptome…

A comprehensive approach to detecting and correcting spurious transcriptome inference due to RNAseq reads misalignment.

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RNA-QC-Chain
Desktop

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…

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Picard
Desktop

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.

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BM-Map
Desktop

BM-Map

A stand-alone, efficient, and user-friendly software package for accurately…

A stand-alone, efficient, and user-friendly software package for accurately allocating multireads.

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QPLOT
Desktop

QPLOT

An automated tool that can facilitate the quality assessment of sequencing run…

An automated tool that can facilitate the quality assessment of sequencing run performance. Taking standard sequence alignments as input, QPLOT generates a series of diagnostic metrics summarizing…

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ReadSpy
Desktop

ReadSpy

A tool for quantifying the uniformity of mapped reads in high-throughput…

A tool for quantifying the uniformity of mapped reads in high-throughput sequencing experiments. ReadSpy directly measures the uniformity of both read position and fragment length, and it explains…

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