Genome sequencing is now a common practice and provides valuable data for plant biology research. While getting the genome sequence is now relatively easy, genome annotation is a more complicated process that requires access to computational pipelines and resources that not all research labs have, nor want to manage. The Genome Sequence Annotation Server (GenSAS, https://www.gensas.org/) is a widely used completely web-based platform for annotating genomes. User-friendly interfaces on the website, paired with access to a computational cluster, allow for any lab with an internet connection to perform structural and functional annotation on any eukaryotic or prokaryotic genome. In addition, GenSAS has integrated instances of Apollo and JBrowse which allows for optional manual curation of the genome annotation. GenSAS projects can be shared with other users allowing for collaborative annotation projects. Within GenSAS users are guided through the annotation steps starting with checking the assembly quality, followed by uploading supporting data, identifying and masking repeats, aligning evidence, gene prediction, choosing the official gene set, functional annotation, and preparation of the final result files. Along the way, the individual tool results can be viewed in JBrowse to help guide the annotation process and ensure that the best results are being moved forward. Some of the annotation tools integrated in GenSAS include BUSCO, RepeatMasker, RepeatModeler, Augustus, BRAKER2, GeneMarkES, BLAST, BLAT, DIAMOND, HISAT2, PASA, RNAammer, tRNAScan-SE, InterProScan, Pfam, SignalP, and TargetP. A complete list of tools can be found at https://www.gensas.org/tools.
Coauthors: Taein Lee – Washington State University; Jodi Humann – Washington State University; Stephen Ficklin – Washington State University; Heidi Hough – Washington State University; Jill Wegrzyn – University of Connecticut; David Neale – University of California Davis