A portable, scalable eukaryotic genome annotation pipeline implemented in Nextflow.
This software is a comprehensive computational pipeline for the annotation of eukaryotic genomes (like protozoan parasites). It performs the following tasks:
- Fast generation of pseudomolecules from scaffolds by ordering and orientating against a reference
- Accurate transfer of highly conserved gene models from the reference
- De novo gene finding as a complement to the gene transfer
- Non-coding RNA detection (tRNA, rRNA, sn(o)RNA, ...)
- Pseudogene detection
- Functional annotation (GO, products, ...)
- ...by transferring reference annotations to the target genome
- ...by inferring GO terms and products from Pfam pHMM matches
- Consistent gene ID assignment
- Preparation of validated GFF3, GAF and EMBL output files for jump-starting manual curation and quick turnaround time to submission
It supports parallelized execution on a single machine as well as on large cluster platforms (LSF, SGE, ...).
The pipeline is built on Nextflow as a workflow engine, so it needs to be installed first:
curl -fsSL get.nextflow.io | bash
With Nextflow installed, the easiest way to use the pipeline is to use the prepared Docker container (https://registry.hub.docker.com/u/satta/annot-nf) which contains all external dependencies.
docker pull satta/annot-nf
Here's how to start an example run using Docker (using the example dataset and parameterization included in the distribution):
$ nextflow run nextflow-io/annot-nf -profile docker
For your own runs, provide your own file names, paths, parameters, etc. as defined in the nextflow.config file.
The reference annotations used in the pipeline need to be pre-processed before they can be used. TODO: add documentation on how to prepare references.
Sascha Steinbiss (ss34@sanger.ac.uk)
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