dlysiak / annot-nf

Eukaryotic genome annotation pipeline implemented in Nextflow

annot-nf

A portable, scalable eukaryotic genome annotation pipeline implemented in Nextflow.

Purpose

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, ...).

Requirements

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

Running the pipeline

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.

Preparing reference annotations

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.

Contact

Sascha Steinbiss ([email protected])

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