Bioinformatics made easy
- Quality Control And Assessment
- De-Novo Assembly
- Repeat Masking
- Gene Finding
- Coding Potential
- Multi-locus Sequence Typing (MLST)
- Fast Variant Calling
- Model & Non-Model Variant Annotation
- Variant Filtering
- Guided Genome-Wide Association Studies
- Supports GBS and WGS data
- Quality Control
- Quantify Expression
- De-Novo Assembly
- RNA-Seq Alignment
- Differential Expression Analysis
- Long-Read Analysis
- Single-Cell RNA-Seq
The All-In-One Bioinformatics Software
OmicsBox is a leading bioinformatics software that offers end-to-end NGS data analysis of genomes, transcriptomes, and metagenomes. The application is used by top private and public research institutions worldwide and allows researchers to easily process large and complex data sets, and streamline their analysis process. It is designed to be user-friendly, efficient, and with a powerful set of tools to extract biological insights from omics data.
Ready to use
The software is structured in different modules, each with a specific set of tools and functions designed to perform different types of analysis, such as de-novo genome assemblies, genetic variation analysis, differential expression analysis, and taxonomic classifications of microbiome data, including the functional interpretation and rich visualizations of results. The functional analysis module, which includes the popular Blast2GO annotation methodology makes OmicsBox particularly suited for non-model organism research. This is demonstrated by over 15k scientific research citations. OmicsBox works out of the box on any standard PC or laptop with Windows, Linux, or Mac.
Genome Analysis Module
The Genome Analysis Module is an efficient and user-friendly toolset to characterizes and analyzes newly sequenced genomes. Quality control is performed using FastQC and Trimmomatic, followed by the assembly of whole genome sequences using popular algorithms such as ABySS, SPAdes, and Flye. BWA and Bowtie2 are used for read alignments, and tools for repeat identification and masking prior to gene prediction are also available. OmicsBox enables visualization of annotations through tracks that combine genome sequences, alignments, intron-exon structure, and variant data.
Genetic Variation Module
The Genetic Variation Module allows for variant calling, filtering, and annotation, as well as genome-wide association studies to associate genetic variations with a particular trait or disease. The module offers two analysis strategies for variant calling and filtering using BCFtools and FreeBayes. The resulting VCF file can be annotated via the Variant Effect Predictor from Ensembl, and guided genome-wide association studies can be executed to identify genetic variations associated with a particular trait. This tool combination outperforms alternatives in recent review studies.
The Transcriptomics Module allows for processing RNA-Seq data from raw reads to functional analysis in a flexible and intuitive way. Quality control is followed by alignment to a reference genome using STAR or BWA or de-novo transcriptome assembly using Trinity. Coding regions can be predicted, and expression can be quantified using HTSeq or RSEM. Statistical packages like NOISeq, edgeR, or maSigPro detect differentially expressed genes. Single-Cell RNA-Seq tools identify cell groups and lineage trajectories. Enrichment analysis is integrated to identify over- and underrepresented biological functions easily.
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Functional Analysis Module
The Metagenomics Module enables the analysis of microbiome data, including assembly, annotation, and classification of metagenomic data. Kraken identifies microorganisms down to the strain level, and MetaSPAdes and MEGAHIT assemble large datasets easily and quickly in the cloud. FragGeneScan and Prodigal identify and extract possible genes and proteins, and functional annotation with various databases is available. Statistical tests can identify differential abundance of taxonomies and biological functions between samples, with rich visualizations to aid in interpretation.
OmicsBox Base Platform
Manage Projects and Files, Access to Cloud Computing, Design, Run and Save Workflows, Visualize Data, Genome Browser, Filter and Sort Large Tables, General Bioinformatics Tools, and More.
- Genome Browser
- FastQC Quality Control Tools
- Generic Charts (Bar, Pie, etc.) and Venn Diagrams
- Access to File Manager, Support Mail, Cloud Usage
- Load, View and Export all supported file types (.box, .b2g, .fasta, . fastq, .gff, .vcf., .bam, etc.)
- Barcode Demultiplexing with Cutadapt