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Assembly evaluation software tools | RNA sequencing data analysis

Ability to generate large RNA-Seq data sets created a demand for both de novo and reference-based transcriptome assemblers. However, while many transcriptome assemblers are now available, there is still no unified quality assessment tool for 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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rnaQUAST
Desktop

rnaQUAST

A tool for evaluating RNA-seq assembly quality and benchmarking transcriptome…

A tool for evaluating RNA-seq assembly quality and benchmarking transcriptome assemblers using reference genome and gene database. rnaQUAST calculates various metrics without using alignment…

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TransRate
Desktop

TransRate

A tool for reference-free quality assessment of de novo transcriptome…

A tool for reference-free quality assessment of de novo transcriptome assemblies. Using only sequenced reads as the input, TransRate measures the quality of individual contigs and whole assemblies,…

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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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SAG-QC
Desktop

SAG-QC

Identifies and excludes non-target sequences independent of database. SAG-QC…

Identifies and excludes non-target sequences independent of database. SAG-QC calculates the probability that a sequence was derived from contaminants by comparing k-mer compositions with the no…

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DETONATE
Desktop
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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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BUSCO
Desktop

BUSCO Benchmarking Universal Single-Copy Orthologs

Provides measures for quantitative assessment of genome assembly, gene set, and…

Provides measures for quantitative assessment of genome assembly, gene set, and transcriptome completeness based on evolutionarily informed expectations of gene content from near-universal…

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IRAP
Desktop

IRAP integrated RNA-seq Analysis Pipeline

A flexible RNA-seq analysis pipeline that allows the user to select and apply…

A flexible RNA-seq analysis pipeline that allows the user to select and apply their preferred combination of existing tools for mapping reads, quantifying expression and testing for differential…

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Junckey
Desktop

Junckey

Calculates proportion spliced index (PSI) values for junction clusters. Junckey…

Calculates proportion spliced index (PSI) values for junction clusters. Junckey uses files produced by STAR as input. It computes junctions thank to the relative inclusion of the nearby junctions.

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