Genomes.

In the last decade, the rise of affordable high-throughput sequencing technologies has led to rapid advances across the biological sciences. At the time of writing, annotated reference genomes are available within most clades of eukaryotic pathogens, and including un-annotated sequences over 550 genomes are available in total. This has greatly facilitated studies in many areas of parasitology. In addition, the volume of functional genomics data, including analysis of differential transcription and DNA-protein interactions, has increased exponentially. With this unprecedented increase in publicly available data, tools to search and compare datasets are also becoming ever more important. A number of database resources are available, and access to these has become fundamental for a majority of research groups. This chapter discusses the current state of genomics research for Author Affiliations: 1 Department of Biology, University of Pennsylvania, Philadelphia USA Email: oharb@upenn.edu Tel: +1 215-746-7019. 2 Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA Email: ucb@sanger.ac.uk. 3 Wellcome Trust Centre for Molecular Parasitology, B6-28 SGDB, 120 University Place, Glasgow, G12 8TA Email: kathryn.crouch@glasgow.ac.uk Tel: +44 141 330 3746. 4 University of Maryland School of Medicine, Insti-tute for Genome Sciences, BioPark II, Room 645, 801 W. Baltimore St., Baltimore, MD 21201 USA JS Email: jcsilva@som.umaryland.edu OI Email: KAbolude@som.umaryland.edu KT Email: KTretina@som.umaryland.edu Tel: +1 410-706-6721. 5 Institute of Integrative Biology, University of Liv-erpool, Liverpool, L69 7ZB, UK Email: F.SilvaFranco@liverpool.ac.uk. 6 Department of Cell and Molecular Biology, Uppsala University, BMC, Box 596, SE-75123, Uppsala, Sweden Email: staffan.svard@icm.uu.se Tel: +46 184714558. 7 Vector Biology Department, Liverpool School of Tropical Medicine, Pembroke Place, Liverpool, L3 5QA, UK. Email: gareth.weedall@lstmed.ac.uk. Corresponding author. This is an Accepted Manuscript of a book chapter published by Springer-Verlag Wien in Molecular Parasitology: Protozoan Parasites and their Molecules, available online: https://www.springer.com/gp/book/9783709114155. © Springer-Verlag Wien 2016 This work is subject to copyright. All rights are reserved by the Publisher, whether the whole or part of the material is concerned, specifically the rights of translation, reprinting, reuse of illustrations, recitation, broadcasting, reproduction on microfilms or in any other physical way, and transmission or information storage and retrieval, electronic adaptation, computer software, or by similar or dissimilar methodology now known or hereafter developed. The use of general descriptive names, registered names, trademarks, service marks, etc. in this publication does not imply, even in the absence of a specific statement, that such names are exempt from the relevant protective laws and regulations and therefore free for general use. The publisher, the authors and the editors are safe to assume that the advice and information in this book are believed to be true and accurate at the date of publication. Neither the publisher nor the authors or the editors give a warranty, express or implied, with respect to the material contained herein or for any errors or omissions that may have been made. Monographs, or book chapters, which are outputs of Wellcome Trust funding have been made freely available as part of the Wellcome Trust's open access policy A uhor M anscrip t