MAKER

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MAKER logo
Status
  • Mature release
  • active development
  • active support
Resources

About MAKER

MAKER is a portable and easy to configure genome annotation pipeline. MAKER allows smaller eukaryotic genome projects and (as of August 2009) prokaryotic genome projects to annotate their genomes and to create genome databases. MAKER identifies repeats, aligns ESTs and proteins to a genome, produces ab initio gene predictions and automatically synthesizes these data into gene annotations with evidence-based quality values. MAKER is also easily trainable: outputs of preliminary runs can be used to automatically retrain its gene prediction algorithm, producing higher quality gene-models on subsequent runs. MAKER's inputs are minimal. Its outputs are in GFF3 or FASTA format, and can be directly loaded into Chado, GBrowse, JBrowse or Apollo.


Additional MAKER options/capabilities include:

  • Map old annotation sets on to new assemblies.
  • Merge multiple legacy annotation sets into a consensus set of annotations.
  • Update existing annotations to take new evidence into account.
  • Tag pre-existing gene models with evidence alignments and quality control metrics to assist in downstream manual curation.
  • Use GFF3 pass-through to include both evidence alignments and predicted gene models from algorithms not natively supported by MAKER.
  • MAKER is MPI capable for rapid parallelization across computer clusters.
  • You can also easily integrate raw InterProScan results into MAKER, which will identify protein domains, add GO functional categories, and help assign putative gene functions to genome annotations. This data then becomes accessible as part of the GFF3 output and can be loaded into a Chado database, GBrowse, or Apollo.

MAKER comes with sample data for testing purposes. See the /data directory in the download. Visit the MAKER website.

Screenshots

View of MAKER annotations in the Apollo genome annotation curation tool. Supporting evidence is shown in the upper dark panel. Gene annotations are shown in the blue panel.

Downloads

MAKER is available as a compressed TAR file from the MAKER website.

Using MAKER

We recommend that users read the MAKER paper [below] and the README file included with the download before installing and using MAKER.

System Requirements

Optional extras:

  • Augustus 2.0 or higher (for eukaryotic genomes)
  • GeneMark-ES (for eukaryotic genomes)
  • FGENESH 2.6 or higher - requires licence (for eukaryotic genomes)
  • GeneMarkS (for prokaryotic genomes)

Installation

An online installation guide is coming soon; please see the README file in the download for instructions.

Documentation

By default, MAKER runs on a single computer. A parallel version, mpi_maker, is also available. To run mpi_maker you will need a message passing interface (MPI) package installed on all participating computers; try MPICH2. Remember to install MPICH2 with the --enable-sharedlibs flag set to the appropriate value .See the MPICH2 Installer's Guide for more information.

Annotations

The MAKER genome annotation pipeline generates several different types of annotations, including

  • Ab initio gene predictions from SNAP, Augustus, FGENESH, and GeneMark
  • Final gene models from MAKER
  • EST alignments from both EXONERATE and BLASTN
  • Protein alignments from EXONERATE and BLASTX
  • Repeats from RepeatMasker and the MAKER internal RepeatRunner

Publications, Tutorials, and Presentations

Publications on or mentioning MAKER

  • MAKER: an easy-to-use annotation pipeline designed for emerging model organism genomes. PMID:18025269 [1]

Tutorials

Presentations

Contacts and Mailing Lists

Mailing List Link Description Archive(s)
MAKER maker-devel MAKER developers and users list. Google, Nabble (2010/05+)

Support for MAKER is provided on a mailing list, and through a Trac-based wiki, bug tracker and code browser.

More on MAKER

See Category:MAKER


  1. Cite error: Invalid <ref> tag; no text was provided for refs named PMID:18025269