Annotation Pipelines for Next-Generation Sequencing Projects

Abstract

Next-generation sequencing technologies has caused an explosion in the availability of genomic sequence data. This creates both opportunities and challenges, not the least within the bioinformatics field. The opportunities include the possibility to sequence and analyze a wide variety of organisms, spanning distant parts of the tree of life. The challenges include dealing with the shorter sequence lengths, the reduced data quality, and training and quality control issues when dealing with completely novel sequences. In this chapter we present the various issues and aspects involved in building a genome annotation pipeline, particularly aiming at next-generation sequencing data.