MAKER: An easy-to-use annotation pipeline designed for emerging model organism genomes

TLDR

Its purpose is to allow investigators to independently annotate eukaryotic genomes and create genome databases. MAKER identifies repeats, aligns ESTs and proteins, produces ab initio gene predictions, and automatically synthesizes these data into gene annotations with evidence-based quality indices; it is easily trainable, uses minimal inputs, and its outputs can be used to create a GMOD database or viewed in Apollo, with its performance compared to other pipelines. We have developed MAKER, used it to annotate the planarian Schmidtea mediterranea genome and create SmedGD, and our results demonstrate that MAKER provides a simple and effective means to convert a genome sequence into a community‑accessible genome database, especially useful for emerging model organism projects lacking extensive bioinformatics resources.

Abstract

We have developed a portable and easily configurable genome annotation pipeline called MAKER. Its purpose is to allow investigators to independently annotate eukaryotic genomes and 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 having evidence-based quality indices. MAKER is also easily trainable: Outputs of preliminary runs are used to automatically retrain its gene-prediction algorithm, producing higher-quality gene-models on subsequent runs. MAKER’s inputs are minimal, and its outputs can be used to create a GMOD database. Its outputs can also be viewed in the Apollo Genome browser; this feature of MAKER provides an easy means to annotate, view, and edit individual contigs and BACs without the overhead of a database. As proof of principle, we have used MAKER to annotate the genome of the planarian Schmidtea mediterranea and to create a new genome database, SmedGD. We have also compared MAKER’s performance to other published annotation pipelines. Our results demonstrate that MAKER provides a simple and effective means to convert a genome sequence into a community-accessible genome database. MAKER should prove especially useful for emerging model organism genome projects for which extensive bioinformatics resources may not be readily available.