MAKER2: an annotation pipeline and genome-database management tool for second-generation genome projects

By Carson Holt, Mark Yandell. BMC Bioinformatics, 2011

1,987 citations recorded by the source corpus.

BackgroundSecond-generation sequencing technologies are precipitating major shifts with regards to what kinds of genomes are being sequenced and how they are annotated. While the first generation of genome projects focused on well-studied model organisms, many of today's projects involve exotic organisms whose genomes are largely terra incognita. This complicates their annotation, because unlike first-generation projects, there are no pre-existing 'gold-standard' gene-models with which to train gene-finders. Improvements in genome assembly and the wide availability of mRNA-seq data are also creating opportunities to update and re-annotate previously published genome annotations. Today's genome projects are thus in need of new genome annotation tools that can meet the challenges and opportunities presented by second-generation sequencing technologies.ResultsWe present MAKER2, a genome annotation and data management tool designed for second-generation genome projects. MAKER2 is a multi-threaded, parallelized application that can process second-generation datasets of virtually any size. We show that MAKER2 can produce accurate annotations for novel genomes where training-data are limited, of low quality or even non-existent. MAKER2 also provides an easy means to use mRNA-seq data to improve annotation quality; and it can use these data to update legacy annotations, significantly improving their quality. We also show that MAKER2 can evaluate the quality of genome annotations, and identify and prioritize problematic annotations for manual review.ConclusionsMAKER2 is the first annotation engine specifically designed for second-generation genome projects. MAKER2 scales to datasets of any size, requires little in the way of training data, and can use mRNA-seq data to improve annotation quality. It can also update and manage legacy genome annotation datasets.

Subfields: Genetics, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/0a5c4da2eee0a753e5782bc88e7dae7877b6a9de

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Citations in the corpus

Araport11: a complete reannotation of the Arabidopsis thaliana reference genome (2016, methodology): “8) (Holt and Yandell, 2011) under default settings to compute AED for each transcript of protein-coding genes, non-coding RNAs, and pseudogenes.”
Mortierella elongata's roles in organic agriculture and crop growth promotion in a mineral soil (2018, methodology): “Gene prediction of the repeat‐masked genome was performed with Marker2 software (Holt & Yandell, 2011).”
BRAKER2: automatic eukaryotic genome annotation with GeneMark-EP+ and AUGUSTUS supported by a protein database (2020, methodology): “Another though computationally expensive way to recover some missed genes is to align proteins from a protein database to the 6-frame translated genomic DNA [39].”
VectorBase: an updated bioinformatics resource for invertebrate vectors and other organisms related with human diseases (2014, methodology): “VectorBase generates gene sets for each organism based on aggregating both ab initio and evidence-based gene predictions using the MAKER system (3).”
Integration of mapped RNA-Seq reads into automatic training of eukaryotic gene finding algorithm (2014, methodology): “Annotators of novel eukaryotic genomes frequently use a pipeline, MAKER2 (25) that includes the three gene prediction tools, Augustus, GeneMark-ES and SNAP that independenly generate gene predictions.”
BRAKER3: Fully automated genome annotation using RNA-seq and protein evidence with GeneMark-ETP, AUGUSTUS and TSEBRA (2023, neutral): “Similar tools that use RNA-seq and protein data are MAKER2 (Holt and Yandell, 2011), FINDER (Banerjee et al., 2021) and Funannotate ( https://github.com/nextgenusfs/funannotate ).”
MAKER-P: A Tool Kit for the Rapid Creation, Management, and Quality Control of Plant Genome Annotations1[W][OPEN] (2013, methodology): “MAKER, unlike existing pipelines, can produce accurate annotations even in the absence of training data (Holt and Yandell, 2011).”
BRAKER1: Unsupervised RNA-Seq-Based Genome Annotation with GeneMark-ET and AUGUSTUS (2016, methodology): “One of the tools that follow this idea is the MAKER2 pipeline (Holt and Yandell, 2011).”
Genome Annotation and Curation Using MAKER and MAKER-P (2014, methodology): “We recommend that users choose the standard build, as previous work (Holt and Yandell, 2011; Campbell et al., 2014) has shown that this build procedure has the best overall accuracy.”
TSEBRA: transcript selector for BRAKER (2021, methodology): “31 When heterogeneous extrinsic evidence sources are available, some genome annotation tools like 32 MAKER2 [20] and GeMoMa [21] integrate these different sources directly into the annotation 33 protocol.”
The Wild Relative of Rice: Genomes and Genomics (2013, methodology): “These genomes are presently being comparatively annotated using a common annotation platform “MAKER” [ 29 ] and a publication is planned for the summer of 2013.”
Genome evolution across 1,011 Saccharomyces cerevisiae isolates (2018, positive): “We independently ran the three individual components (RATT 56 , YGAP 57 and MAKER 58 ) for gene annotation, and subsequently integrated their results using EVM 59 .”