We are happy to announce OmicsBox 4.1, a new update to BioBam’s OmicsBox platform. The release adds long reads genome assembly tools like Hifiasm and EviAnn to the genome analysis module, brings WikiPathways into functional analysis, and introduces limma for differential expression of proteomics, microarray and RNA-seq data. It also extends CloudSync to eight more tools and makes everyday work simpler, from signing in to choosing files.
The Genome Analysis module gains two new tools that work together. Hifiasm performs haplotype-resolved de novo assembly from PacBio HiFi or Oxford Nanopore long reads, with Trio Binning and Hi-C phasing to fully resolve both haplotypes. EviAnn then annotates eukaryotic genomes from RNA-seq or transcript evidence combined with protein homology. It needs no repeat masking or species-specific training, and produces GFF3 that passes NCBI submission checks. Both tools run with CloudSync, so long assemblies continue even after OmicsBox is closed.
In Transcriptomics, the new Differential Expression Analysis with limma covers quantitative proteomics intensities (label-free, TMT/iTRAQ, DIA/DDA), microarray data and RNA-seq counts. For mass-spectrometry proteomics, the optional DEqMS model accounts for the number of peptides or PSMs behind each protein. For long-read transcriptomes, TUSCO benchmarks reconstructed transcripts against universal single-copy orthologs. In Functional Analysis, WikiPathways is now available in the Combined Pathway Analysis alongside Reactome and Gramene, with improved database and species coverage.
Finally, CloudSync now also supports Minimap2, STARsolo, FLAIR, TAMA Merge, SQANTI3, MEGAHIT, RepeatMasker and Merge VCF. A simplified, account-based login, file dialogs with side-panel bookmarks and a closer integration of Cloud Files round off the release.
OmicsBox 4.1 Release Notes:
Functional analysis
- New WikiPathways database in the Combined Pathway Analysis
- Improved Combined Pathway Analysis database and species coverage
Transcriptomics
- New differential expression analysis with limma for proteomics, microarray and RNA-seq data
- New long-read transcriptome benchmarking with TUSCO
- Improved Gene Co-expression Network analysis with editable hub gene symbols
Genome analysis
- New genome assembly with Hifiasm for long reads, including haplotype-resolved assemblies
- New evidence-based genome annotation with EviAnn
General
- Simplified account-based login
- File dialogs now with side-panel bookmarks
- New CloudSync support for Minimap2, STARsolo, FLAIR, TAMA Merge, SQANTI3, MEGAHIT, RepeatMasker and Merge VCF
- Improved Cloud Files integration
- Multiple minor bug fixes
Step-by-step instructions for each tool are available in the OmicsBox user manual.
About OmicsBox
OmicsBox is BioBam’s bioinformatics software for the analysis of omics data. It provides out-of-the-box workflows for genomics datasets, organised in five modules: Genome analysis, Transcriptomics, Genetic Variation, Functional analysis, and Metagenomics. The Functional analysis module is based on the Blast2GO annotation methodology, with more than 10k citations in the scientific literature, and is widely used in non-model organism research. Computationally demanding steps, such as genome assemblies and other CPU- or memory-intensive pipelines, are executed in the cloud. OmicsBox itself runs on a standard PC or laptop under Windows, Linux, or macOS. Licensing is subscription-based, with flexible options.
Feedback, questions, and feature requests are welcome at support@biobam.com or through the BioBam account. Further information, documentation, and contact options are available at biobam.com/omicsbox and in the user manual. Trade names: BioBam, OmicsBox, and Blast2GO as used by BioBam.
