Edit Tool data: MAKER

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The Basics[edit]

Name:
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Tool classification or features:	Genome Annotation
Platform:	If the tool linux unix os x windows web vm cloud
Brief description:	MAKER is an easy-to-configure, portable genome [[:Category:Annotation\|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 [[Glossary#FASTA\|FASTA]] format, and can be directly loaded into [[Chado]], [[GBrowse]], [[JBrowse]], [[WebApollo]] or [[Apollo]]. For those annotating novel plant genomes, the [http://www.yandell-lab.org/software/maker-p.html 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 [http://www.yandell-lab.org/software/maker-p.html 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 <abbr title="message-passing interface">MPI</abbr>-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 <tt>/data</tt> directory in the download.
Open source:
Software licence:
Type of input data	e.g. genomic sequence; taxonomic group; protein identifier; anatomy ontology, etc.
Input formats:	[[GFF3]], [[Glossary#FASTA\|FASTA]]
Output formats:	[[GFF3]], [[Glossary#FASTA\|FASTA]]
Programming language(s)
Intended usage
First public release
Use standard tool display template?	yes

Files[edit]

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Contact details[edit]

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Materials[edit]

Publications	MAKER-P: a tool-kit for the rapid creation, management, and quality control of plant genome annotations. <ref name=PMID:24306534 /> MAKER2: an annotation pipeline and genome-database management tool for second-generation genome projects. <ref name=PMID:22192575 /> *MAKER: an easy-to-use annotation pipeline designed for emerging model organism genomes. <span class="Z3988" title="ctx_ver=Z39.88-2004&rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&rfr_id=info%3Asid%2Focoins.info%3Agenerator&rft.genre=article&rft_id=info%3Apmid%2F18025269">PMID:18025269</span> <ref name=PMID:18025269/>
Presentations	* [[:Image:MAKERSMBE2009.pdf\|MAKER—the easy-to-use genome annotation pipeline]], presented by Mark Yandell at the [http://ccg.biology.uiowa.edu/smbe/symposia.php?action=view&sym_ID=27 SMBE 2009 GMOD Workshop].
Tutorials	;[[MAKER Tutorial]] :taught as part of the [[2013 GMOD Summer School]] [https://pods.iplantcollaborative.org/wiki/display/sciplant/MAKER-P+at+iPlant MAKER at iPlant] :how to access MAKER using Atmosphere cloud image and TACC Lonestar

Extra Textual Goodies[edit]

Any introductory text for users	We recommend that users read the MAKER paper [below] and the README file included with the download before installing and using MAKER.
Software prerequisites	* Perl 5.8.0 or higher * [[BioPerl]] 1.6 or higher. * [http://blast.wustl.edu WU-BLAST] 2.0 or higher or [http://www.ncbi.nlm.nih.gov/ NCBI-BLAST] 2.2.X or higher * [http://www.repeatmasker.org/ RepeatMasker] 3.1.6 or higher ** RepeatMasker requires a repeat library, available from [http://www.girinst.org/repbase/index.html Repbase]. * [http://www.animalgenome.org/bioinfo/resources/manuals/exonerate/ Exonerate] 1.4 or higher. Optional extras: * [http://korflab.ucdavis.edu/software.html SNAP] version 2009-02-03 or higher (for eukaryotic genomes). * [http://augustus.gobics.de Augustus] 2.0 or higher (for eukaryotic genomes) * [http://exon.biology.gatech.edu GeneMark-ES] (for eukaryotic genomes) * [http://www.softberry.com FGENESH] 2.6 or higher - requires licence (for eukaryotic genomes) * [http://exon.biology.gatech.edu GeneMarkS] (for prokaryotic genomes)
Installation	Please see the [http://www.yandell-lab.org/software/maker_install.html installation guide] or the README file in the download for instructions.
Configuration
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 [http://en.wikipedia.org/wiki/Message_Passing_Interface message passing interface (MPI)] package installed on all participating computers; try [http://www.mcs.anl.gov/research/projects/mpich2/ MPICH2]. Remember to install MPICH2 with the <tt>--enable-sharedlibs</tt> flag set to the appropriate value .See the [http://www.mcs.anl.gov/research/projects/mpich2/documentation/index.php?s=docs MPICH2 Installer's Guide] for more information. See also the [http://www.yandell-lab.org/software/maker-p.html MAKER-P website] for documentation on the additional pipeline steps for annotating plant genomes. === 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
Development team	Yandell Lab, Utah; Ian Korf (University of California Davis)
Development status
Download/usage tracking
Logo info
See also	Any extra information, links, etc. Almost all the ant genomes at the [http://hymenopteragenome.org/ant_genomes/ Ant Genomes Portal] were independently annotated with MAKER.
Extra items for component box

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[[Category:GMOD Components]] [[Category:Annotation]] [[Category:MAKER]]

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