MAKER specifications

Information


Unique identifier OMICS_13535
Alternative name MAKER2
Interface Web user interface
Restrictions to use Academic or non-commercial use
Input data Genome sequences, annotations
Input format FASTA, GFF3
License Artistic License version 2.0, GNU General Public License version 3.0
Computer skills Basic
Version 1.0
Stability Stable
Maintained Yes

Documentation


Maintainer


  • person_outline Mark Yandell <>

Information


Unique identifier OMICS_13535
Alternative name MAKER2
Software type Pipeline/Workflow
Interface Graphical user interface
Restrictions to use Academic or non-commercial use
Input data Genome sequences, annotations
Input format FASTA, GFF3
Operating system Unix/Linux, Mac OS
Programming languages Perl
License Artistic License version 2.0, GNU General Public License version 3.0
Computer skills Medium
Version 2.31.8
Stability Stable
Requirements SNAP, RepeatMasker, Exonerate, NCBI BLAST
Maintained Yes

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Documentation


Maintainer


  • person_outline Mark Yandell <>

MAKER article

MAKER citations

 (3)
2018
PMCID: 5756342

[…] maximum scaffold size of 151,286 bp. the completeness of the assembly was assessed using busco v12 [32], which estimated the genome sequence to be 99.65% complete. the genome was annotated using the maker2 pipeline [33]. overall, 13,139 protein-coding gene models were predicted., the new genome assembly of d. helianthi strain 7/96 is present in genbank with accession number: mavt00000000.2., […]

2017
PMCID: 5824900

[…] of multiexon genes, small rnas, and lncrnas. an optimized workflow to annotate protein-coding genes and their isoforms is shown in figure 1. to take advantage of the extensive rna-seq datasets, maker2, specifically designed for second-generation genome projects, was first used to generate an initial protein-coding gene annotation.15 input data for maker2 include (i) repeats masked genome […]

2017
PMCID: 5737241

[…] and a. fragilis are available as is a set of tracks representing elements conserved between s. purpuratus (figure 5). other genomes such as l. variegatus, p. miniataand p. parvimensis have contigs, maker2 predicted gene models and genomic repetitive sequence tracks. , a survey of putative open chromatin regions in sp embryonic stage nuclei determined by the atac-seq strategy are shown […]

MAKER institution(s)
Eccles Institute of Human Genetics, University of Utah, Salt Lake City, UT, USA; Ontario Institute for Cancer Research, MaRS Centre, ON, Canada
MAKER funding source(s)
This work was supported by the grants NIH/NHGRI-R01-HG004694 and NSF IOS-1126998 and partially supported by the NIH Genetics Training Grant T32-GM007464.

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