W093MAKER: The Easy-to-use Genome Annotation Pipeline
Time: 11:10 AM
Carson Holt, Daniel Ence, Barry Moore, Mark Yandell
University of Utah, Utah Center for Genetic Discover, Salt Lake City UT
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. MAKER's inputs are minimal, and its outputs are GFF3 and FASTA files that can be used by Chado, Gbrowse, JBrowse, or Apollo. We will present highlights from some recently annotated genomes, and explain how we are now integrating MAKER with resequencing efforts to enable rapid genotype-phenotype association.