OmicsBox now includes EviAnn for structural annotation of eukaryotic genomes. EviAnn derives gene models from transcript alignments and protein homology instead of ab initio prediction, so it requires neither species-specific training nor repeat masking.
What is EviAnn
EviAnn (Evidence-based Annotation) is a structural annotation pipeline for eukaryotic genomes developed by Zimin, Puiu, Pertea, Yorke and Salzberg at Johns Hopkins University (Nature Methods, 2026).
Most annotation pipelines, such as BRAKER and MAKER, rely on ab initio gene predictors. These predictors must be trained for each species, and the genome must first be repeat-masked with a species-specific repeat library. For non-model organisms, both steps are slow, sensitive to parameter choices, and often the main bottleneck of a genome project.
EviAnn removes these steps. It builds gene models directly from experimental evidence: transcripts are reconstructed from RNA-seq alignments, proteins from related species are aligned to the genome, and coding sequences are defined where transcript and protein evidence agree. Loci supported only by protein alignments are added as gene models, and expressed transcripts without coding potential are reported as long non-coding RNAs (lncRNAs).
Main advantages:
- No training or repeat masking: results depend on the evidence supplied, not on a species-specific model.
- Accuracy: in the authors’ benchmarks, EviAnn was more accurate than BRAKER3, MAKER2 and FINDER.
- Speed: lower computational cost than these pipelines.
- Protein-coding genes and lncRNAs annotated in a single run.
- Large genomes: supports assemblies up to 32 Gbp.
EviAnn is particularly useful for newly assembled genomes of non-model species for which RNA-seq data are available but no trained gene predictor or repeat library exists. It is also well suited to large, repeat-rich genomes, such as many plant genomes.
How to run EviAnn in OmicsBox
EviAnn is available in OmicsBox, a desktop application for NGS data analysis that requires no programming. Input files and parameters are selected in its graphical interface, and EviAnn and its dependencies do not need to be installed.
The tool is located under Genome Analysis → Gene Finding → Eukaryotic Gene Finding (select EviAnn). To run an annotation you need:
- Genome assembly in FASTA format.
- Transcript evidence: Illumina RNA-seq reads, PacBio Iso-Seq reads, or aligned BAM files. Without RNA-seq, transcripts from a closely related species (>95% DNA identity) can be used.
- Proteins from related species (recommended). If none are provided, UniProt proteins are used.
The annotation strategy follows from the evidence supplied, so there is no mode to select. Options such as ploidy, maximum intron size and minimum lncRNA expression can be adjusted when needed.
Monitoring the analysis progress
The analysis runs on the OmicsBox cloud, so no local setup or computing cluster is required. Large genomes are processed on cloud resources, which reduces run time.
With CloudSync, OmicsBox only needs to be open to configure and submit the job. OmicsBox can then be closed and the computer shut down while the analysis continues in the cloud. An email notification can be requested when the job finishes, and results can be saved to Cloud Files to open them from any device signed in with the same account.
With OmicsBox Web, the progress of an analysis can be checked at any time and from anywhere: a laptop, tablet or phone with a browser is enough, with no installation. The Jobs page shows the status, progress, run time and logs of each analysis, and running jobs can be cancelled. Once the job is done, results can be previewed directly in the browser, so a first look at the annotation does not have to wait until you are back at your desk.
Results
EviAnn results are written in standard formats, so they can be used in genome browsers, other annotation tools or NCBI submission without conversion:
- GFF3 annotation with gene, mRNA, exon, CDS and lncRNA features.
- FASTA files of predicted proteins and transcripts.
Within OmicsBox, a summary report lists the parameters used and provides useful summary statistics. Charts can be configured within the platform and exported to high-quality png or pdf for presentations or publications. The GFF3 annotation can be inspected directly in OmicsBox.
Predicted proteins can be passed directly to the Blast2GO pipeline for functional annotation.
Availability
EviAnn is available in the Genome Analysis module. All parameters are described in the EviAnn user manual.
Reference: Zimin AV, Puiu D, Pertea M, Yorke JA, Salzberg SL. Efficient evidence-based genome annotation with EviAnn. Nature Methods 23(8), 1521–1527 (2026).