Maker: The Easy-to-Use Genome Annotation Pipeline

MAKER is a portable and easy-to-use genome annotation pipeline and annotation management tool. MAKER identifies repeats; aligns ESTs, RNA-seq data, 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 easily trainable: outputs of preliminary runs can be used to automatically retrain its gene prediction algorithms, producing higher quality gene-models on subsequent runs. MAKER is also a genome management tool that can update legacy annotations using new experimental evidence, such as mRNA-seq data; it can also map annotations forward to updated genome assemblies. Many of these functionalities were employed in the annotation of the most recent version (V4) of the maize (B73) genome. MAKER's inputs are minimal, and its outputs are GFF3 and FASTA files that can be used by other GMOD tools such as Chado, Gbrowse, JBrowse, and Apollo.