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 assemblies.
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 metagenomics. The software enables to generate custom workflows, which can combine quality control steps, adapter trimming, read mapping, variant detection, and multiple filtering and annotation steps into a pipeline.
Provides measures for quantitative assessment of genome assembly, gene set, and transcriptome completeness based on evolutionarily informed expectations of gene content from near-universal single-copy orthologs selected from OrthoDB. BUSCO assessments are implemented in open-source software, with comprehensive lineage-specific sets of benchmarking universal single-copy orthologs for arthropods, vertebrates, metazoans, fungi, eukaryotes, and bacteria.
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, enabling assembly optimization and comparison. TransRate can accurately evaluate assemblies of conserved and novel RNA molecules of any kind in any species.
A methodology and corresponding software package for evaluating de novo transcriptome assemblies, which can compute both reference-free and reference-based measures. DETONATE consists of two component packages, RSEM-EVAL and REF-EVAL. Both packages are mainly intended to be used to evaluate de novo transcriptome assemblies, although REF-EVAL can be used to compare sets of any kinds of genomic sequences.
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 samples, allowing detection of subtle differences not noticeable when switching between different files. Data visualization aids batch effect detection and minimizes the risk of confounding factors affecting the results of the study.
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 information, e.g. length distribution and N50 of the assembled transcripts. Additionally, rnaQUAST computes the following statistics for the gene database: the total number of genes and isoforms, isoform and exon length distribution, average number of exons per gene, etc. It outputs metrics in a user-friendly report.
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 expression. iRAP also includes multiple tools for gene set enrichment analysis and generates web browsable reports of the results obtained in the different stages of the pipeline. Depending upon the application, iRAP can be used to quantify expression at the gene, exon or transcript level.