afterParty: turning raw transcriptomes into permanent resources

BACKGROUND: Next-generation DNA sequencing technologies have made it possible to generate transcriptome data for novel organisms quickly and cheaply, to the extent that the effort required to annotate and publish a new transcriptome is greater than the effort required to sequence it. Often, following publication, details of the annotation effort are only available in summary form, hindering subsequent exploitation of the data. To promote best-practice in annotation and to ensure that data remain accessible, we have written afterParty, a web application that allows users to assemble, annotate and publish novel transcriptomes using only a web browser. RESULTS: afterParty is a robust web application that implements best-practice transcriptome assembly, annotation, browsing, searching, and visualization. Users can turn a collection of reads (from Roche 454 chemistry) or assembled contigs (from any sequencing chemistry, including Illumina Solexa RNA-Seq) into a searchable, browsable transcriptome resource and quickly make it publicly available. Contigs are functionally annotated based on similarity to known sequences and protein domains. Once assembled and annotated, transcriptomes derived from multiple species or libraries can be compared and searched. afterParty datasets can either be created using the existing afterParty server, or using local instances that can be built easily using a virtual machine. afterParty includes powerful visualization tools for transcriptome dataset exploration and uses a flexible annotation architecture which will allow additional types of annotation to be added in the future. CONCLUSIONS: afterParty's main use case scenario is one in which a working biologist has generated a large volume of transcribed sequence data and wishes to turn it into a useful resource that has some durability. By reducing the effort, bioinformatics skills, and computational resources needed to annotate and publish a transcriptome, afterParty will facilitate the annotation and sharing of sequence data that would otherwise remain unavailable. A typical metazoan transcriptome containing several tens of thousands of contigs can be annotated in a few minutes of interactive time and a few days of computational time.