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):
$ git clone https://github.com/satta/annot-nf.git
$ cd annot-nf
$ ROOTDIR=`pwd` nextflow -c loc_docker.config -c params_default.config run annot.nf
For your own runs, clone params_default.config
and substitute your own file names, paths, parameters, etc.
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 ([email protected])
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