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Last pushed: 2 years ago
Short Description
A Docker execution environment for Companion.
Full Description


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, ...)
    • transferring reference annotations to the target genome
    • 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 | bash

With Nextflow installed, the easiest way to use the pipeline is to use the prepared Docker container ( which contains all external dependencies.

docker pull sangerpathogens/companion

Running the pipeline

Here's how to start an example run using Docker (using the example dataset and parameterization included in the distribution):

$ nextflow run sanger-pathogens/companion -profile docker

For your own runs, provide your own file names, paths, parameters, etc. as defined in the nextflow.config file.

Preparing reference annotations

The reference annotations used in the pipeline need to be pre-processed before they can be used.
See the HOWTO on the GitHub wiki for more details. There are also pre-generated reference sets for various parasite species/families. Please contact the authors via the email address below to obtain them.


Sascha Steinbiss (

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