- Mature release
- Development: active
- Support: active
MAKER is an easy-to-configure, portable genome annotation pipeline. MAKER allows smaller eukaryotic genome projects and 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, WebApollo or Apollo.
For those annotating novel plant genomes, the MAKER-P pipeline is designed to make the annotation tractable for small groups with limited bioinformatics experience and resources, and faster and more transparent for large groups with more experience and resources. The MAKER-P pipeline generates species-specific repeat libraries, as well as structural annotations of protein coding genes, non-coding RNAs, and pseudogenes. The MAKER-P website has more information on the additional protocols for plant genome annotation.
Additional MAKER options and 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, JBrowse, GBrowse, WebApollo or Apollo.
MAKER comes with sample data for testing purposes. See the /data directory in the download.
Visit the MAKER website.
We recommend that users read the MAKER paper [below] and the README file included with the download before installing and using MAKER.
- Perl 5.8.0 or higher
- BioPerl 1.6 or higher.
- WU-BLAST 2.0 or higher or NCBI-BLAST 2.2.X or higher
- RepeatMasker 3.1.6 or higher
- RepeatMasker requires a repeat library, available from Repbase.
- Exonerate 1.4 or higher.
- SNAP version 2009-02-03 or higher (for eukaryotic genomes).
- 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)
Please see the installation guide or the README file in the download for instructions.
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.
See also the MAKER-P website for documentation on the additional pipeline steps for annotating plant genomes.
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-P: a tool-kit for the rapid creation, management, and quality control of plant genome annotations. 
- MAKER2: an annotation pipeline and genome-database management tool for second-generation genome projects. 
- MAKER: an easy-to-use annotation pipeline designed for emerging model organism genomes. PMID:18025269 
- how to access MAKER using Atmosphere cloud image and TACC Lonestar
- MAKER—the easy-to-use genome annotation pipeline, presented by Mark Yandell at the SMBE 2009 GMOD Workshop.
Contacts and Mailing Lists
|Mailing List Link||Description||Archive(s)|
|MAKER||maker-devel||MAKER developers and users list.||Bluehost, Google, Nabble (2010/05+)|
Yandell Lab, Utah; Ian Korf (University of California Davis)
Almost all the ant genomes at the Ant Genomes Portal were independently annotated with MAKER.
More on MAKER
- MAKER-P: a tool-kit for the rapid creation, management, and quality control of plant genome annotations. Plant Physiol. 2013
- MAKER2: an annotation pipeline and genome-database management tool for second-generation genome projects. BMC Bioinformatics 2011 12 491
- MAKER: an easy-to-use annotation pipeline designed for emerging model organism genomes. Genome Res. 2008 18 188-96