nf-core pipeline · annotation, assembly, draft-genome
nf-core/genomeannotator
Identifies coding gene structures in eukaryotic draft genomes using external evidence and ab initio models.
What nf-core/genomeannotator is
nf-core/genomeannotator is a bioinformatics pipeline designed to identify gene structures, particularly coding sequences, in draft eukaryotic assemblies. Although created with an emphasis on metazoans, it is structured to accommodate other eukaryotic groups.
The pipeline was originally developed by Marc P. Hoeppner with contributions from Montserrat Torres-Oliva. It addresses the challenge of resolving complex gene structures in newly assembled or uncharacterised genomes by integrating multiple lines of biological evidence, including protein alignments, transcripts, and RNA-seq data, into a combined consensus build.
Note that nf-core/genomeannotator has been deprecated and is no longer maintained, with a replacement workflow under development.
What the pipeline does
The workflow begins by preprocessing the genome assembly, filtering out small contigs and cleaning sequence identifiers. External evidence sources, including proteins, transcripts, and RNA-seq reads, are aligned to the assembly and subsequently converted into annotation support data.
Using these alignments, gene models are predicted using AUGUSTUS, with the option to incorporate PASA. When selected, optional de novo transcriptome assembly can be carried out using Trinity, and synteny-based annotation mapping from related genomes can be performed using Satsuma2 and Kraken. Finally, EvidenceModeler synthesises the predictions and evidence into a consensus gene set.
Key facts
- Pipeline engine
- Nextflow (DSL2)
- Original author
- Marc P. Hoeppner
- Target organisms
- Eukaryotes, focusing on metazoans
- Supported inputs
- Draft genome assemblies, RNA-seq, transcripts, and protein sequences
- Gene model predictors
- AUGUSTUS, PASA (optional)
- Consensus builder
- EvidenceModeler
- Status
- Deprecated and unmaintained
What you can use it for
- Draft genome annotation
- Predicting coding gene structures across newly assembled eukaryotic or metazoan contigs.
- Evidence-driven gene modelling
- Combining RNA-seq data, transcript sequences, and cross-species protein alignments to generate supported gene models via AUGUSTUS and EvidenceModeler.
- Synteny-based annotation transfer
- Transferring gene structures from related reference genomes using Satsuma2 and Kraken.
- De novo transcriptome-assisted annotation
- Generating de novo transcript assemblies with Trinity to provide empirical evidence for gene prediction.
Run it here
The research agent runs nf-core/genomeannotator with Nextflow on its own machine — up to 32 cores, 256 GiB of memory and 24 hours per run, which covers the test profile and real single-sample runs. It builds the samplesheet, checks it against the pipeline's schema and reads the results back. When a run is too big for one machine, it gives you the exact command for your own cluster instead.
Strengths and limits
Good at
- Integrates empirical evidence from RNA-seq, transcripts, and proteins with ab initio gene predictions.
- Uses EvidenceModeler to reconcile multiple conflicting predictions into a consensus gene build.
- Implements Nextflow DSL2 with individual containerised processes to maintain software reproducibility.
- Accommodates optional upstream steps including Trinity de novo transcript assembly and Satsuma2 synteny mapping.
Watch out for
- The pipeline is deprecated and no longer receives updates or maintenance.
- Optimised primarily for metazoans, which may require manual adjustments when run on other eukaryotic lineages.
- Requires Nextflow version 21.10.3 or higher to run.
Questions
Can I run nf-core/genomeannotator without my own cluster?
The research agent runs nf-core/genomeannotator with Nextflow on its own machine — up to 32 cores, 256 GiB of memory and 24 hours per run, which covers the test profile and real single-sample runs. It builds the samplesheet, checks it against the pipeline's schema and reads the results back. When a run is too big for one machine, it gives you the exact command for your own cluster instead.
What licence is nf-core/genomeannotator under?
MIT, like every nf-core pipeline.
Is nf-core/genomeannotator actively maintained?
No, the pipeline is deprecated and no longer maintained. A replacement pipeline is being developed.
Can the pipeline annotate non-metazoan organisms?
Yes. It was designed with a focus on metazoans, but other eukaryotic groups are supported.
What tools are used to predict gene structures?
Gene models are constructed using AUGUSTUS and optionally PASA, followed by EvidenceModeler to create the final consensus annotations.
Can RNA-seq reads be assembled directly within the pipeline?
Yes, de novo transcriptome assembly can be optionally executed using Trinity.
Can annotations from related organisms be used?
Yes, the pipeline supports optional annotation mapping from related genomes via Satsuma2 and Kraken.
How to cite it
Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen. The nf-core framework for community-curated bioinformatics pipelines. Nat Biotechnol. 2020 Feb 13. doi: 10.1038/s41587-020-0439-x.
Written from nf-core/genomeannotator's own README. Statements citing a figure that does not appear there are removed before publication. Licence and running details come from our registry.