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Bioinformatics: Software

P0340
Multi-Trait Genome Wide Association Tests Result in a Reduction in False Positives
Anthony Greenberg, Bayesic Research; Jean-Luc Jannink, USDA-ARS / Cornell University; Susan McCouch, Cornell University

P0341
BUSCO: Assessing Genome Assembly and Annotation Completeness with Single-Copy Orthologs
Felipe A. Simão, Swiss Institute of Bioinformatics; Robert M. Waterhouse, University of Geneva Medical School & Swiss Institute of Bioinformatics; Panagiotis Ioannidis, Department of Genetic Medicine and Development, University of Geneva Medical School; Evgenia V. Kriventseva, Department of Genetic Medicine and Development, University of Geneva Medical School; Evgeny M. Zdobnov, Department of Genetic Medicine and Development, University of Geneva Medical School

P0342
solGS: A Web-based Solution for Genomic Selection
Isaak Y. Tecle, Boyce Thompson Institute for Plant Research; Naama Menda, Boyce Thompson Institute for Plant Research; Lukas Mueller, Boyce Thompson Institute for Plant Research

P0343
AgroPortal : A Proposition for Ontology-Based Services in the Agronomic Domain
Clement Jonquet, Laboratory of Informatics, Robotics, and Microelectronics of Montpellier (LIRMM); Esther Dzalé-Yeumo, French National Institute for Agricultural Research (INRA); Elizabeth Arnaud, Bioversity International; Pierre Larmande, IRD, UMR DIADE, Institut de Biologie Computationnelle; Anne Toulet, University of Montpellier - LIRMM; Marie-Angélique Laporte, Bioversity International

P0344
NDEx: Sharing and Publishing Biological Networks for Any Species
Dexter Pratt, UC San diego

P0345
PlantTribes: A Collection of Automated Plant Gene Family Analysis Pipelines
Eric Kenneth Wafula, Penn State University; Joshua P. Der, California State University, Fullerton; Loren Honaas, Penn State University; Saravanaraj Ayyampalayam, The University of Georgia; Norman Wickett, Chicago Botanic Garden; Jim Leebens-Mack, University of Georgia; Claude dePamphilis, Penn State University

P0346
Highly Interactive Data Analysis and Productivity (HIDAP) tools for Breeding
Reinhard Simon, International Potato Center (CIP); Omar Benites, International Potato Center (CIP); Raul Eyzaguirre, International Potato Center (CIP); Awais Khan, International Potato Center; Luka Wanjohi, International Potato Center (CIP)

P0348
Field Book: An Open-Source Android App for Collecting Phenotypic Data
Trevor W. Rife, Kansas State University; Jesse Poland, Kansas State University

P0349
TheSNPpit - A Multi Panel SNP Data Management Package
Eildert Groeneveld, Institute of Farm Animal Genetics (FLI); Helmut Lichtenberg, Institute of Farm Animal Genetics (FLI)

P0350
An RNA-Seq Analysis Pipeline for Switchgrass Integrating Co-Expression Network Analysis
Qin Ma, South Dakota State University

P0351
Functional Annotation of Alternative Splicing in Plants by the AStafunk Pipeline
Michael Sammeth, Institute of Biophysics / Federal University of Rio de Janeiro; Vitor L. Coelho, Federal University of Rio de Janeiro

P0352
Mango: An Environment for Combining Massive Heterogeneous Networks
Jennifer Chang, Iowa State University; Hui-Hsien Chou, Iowa State University; Hyejin Cho, Iowa State University

P0353
A New Streamlined Workflow for De Novo Transcriptome Assembly and Annotation in Non-Model Organisms
Matthew Keyser, DNASTAR, Inc.

P0354
Fast-GBS: A New Pipeline for the Efficient and Accurate Calling of SNPs from Genotyping-By-Sequencing Data
Davoud Torkamaneh, Laval University; Francois Belzile, Laval University; Jérôme Laroche, Université Laval

P0355
VirusDetect: Efficient and Accurate Discovery of Virus By Deep Sequencing of Small RNAs
Yi Zheng, Boyce Thompson Institute for Plant Research; Shan Gao, Nankai University; Kai-Shu Ling, USDA-ARS, U.S. Vegetable Laboratory; Jan Kreuze, International Potato Center; Zhangjun Fei, Boyce Thompson Institute for Plant Research, Cornell University

P0356
Web-Based Bioinformatics Workflows for RNA-Seq Data Analysis in Agricultural Animal Species
Weizhong Li, J Craig Venter Institute; Robert W. Li, ARS, USDA; Alexander Richter, J Craig Venter Institute

P0357
Rascaf: Improving Genome Assembly with RNA-seq Data
Liliana Florea, Johns Hopkins University School of Medicine; Li Song, Johns Hopkins University; Dhruv Shankar, University of North Carolina

P0358
fRNAkenseq: a Powered-by-iPlant RNA Sequencing Analysis Platform
Allen Hubbard, University of Delaware; Wayne Treible, University of Delaware; Matthew Bomhoff, University of Arizona; Eric Lyons, University of Arizona; Carl J. Schmidt, University of Delaware

P0359
Lighter and Rcorrector: Tools for Next Generation Sequencing Error Correction
Li Song, Johns Hopkins University; Ben Langmead, Johns Hopkins University School of Medicine; Liliana Florea, Johns Hopkins University School of Medicine

P0360
A Bioinformatics Tool Searching for Genome-Wide SSR Markers by Using High-Throughput Sequencing Data
Masaaki Kobayashi, School of Agriculture, Meiji University; Kentaro Yano, School of Agriculture, Meiji University

P0362
Bioinformatic Analysis of Genotype by Sequencing (GBS) Data with NGSEP
Claudia Samantha Perea de La Torre, International Center for Tropical Agriculture (CIAT); Juan Fernando De la Hoz, International Center for Tropical Agriculture (CIAT); Daniel F. Cruz, International Center for Tropical Agriculture (CIAT); Juan David Lobaton, International Center for Tropical Agriculture (CIAT); Paulo Izquierdo, International Center for Tropical Agriculture (CIAT); Juan Camilo Quintero, International Center for Tropical Agriculture (CIAT); Bodo Raatz, International Center for Tropical Agriculture (CIAT); Jorge A. Duitama Castellanos, International Center for Tropical Agriculture (CIAT)

P0363
A GUI Application 'CA Plot Viewer' for Large-Scale Gene Expression Analysis and Databases for Gene Expression Networks
Kentaro Yano, School of Agri., Meiji University; Shin Terashima, School of Agri., Meiji University; Yukino Nakamura, School of Agri., Meiji University; Minami Katayama, School of Agri., Meiji University; Yuno Takaki, School of Agri., Meiji University; Kataru Onosato, School of Agri., Meiji University; Tomoyuki Takano, School of Agri., Meiji University; Yohei Sasaki, School of Agri., Meiji University; Maasa Kanno, School of Agri., Meiji University; Misa Saito, School of Agriculture, Meiji University; Noriko Matsuda, School of Agri., Meiji University; Satomi Asano, School of Agriculture, Meiji University; Koji Yokoyama, School of Agri., Meiji University; Yoshifumi Tada, TOHOKU CHEMICAL CO., LTD.; Hiroshi Chiba, TOHOKU CHEMICAL CO., LTD.; Hajime Ohyanagi, School of Agri., Meiji University; Toru Kudo, School of Agri., Meiji University; Masaaki Kobayashi, School of Agri., Meiji University

P0364
GenSAS v4.0: An Easy-to-Use, Web-Based Platform for Structural and Functional Genome Annotation and Curation
Jodi L. Humann, Washington State University; Stephen P. Ficklin, Washington State University; Taein Lee, Washington State University; Chun-Huai Cheng, Washington State University; Sook Jung, Washington State University; Jill Wegrzyn, Department of Ecology and Evolutionary Biology, University of Connecticut; David Neale, Dept. Plant Sciences University of California Davis; Dorrie Main, Washington State University

P0365
GVCHAP: A Computer Package for Genomic Prediction and Estimation Using Haplotypes and Single SNPs
Dzianis Prakapenka, Department of Animal Science, University of Minnesota; Chunkao Wang, Department of Animal Science, University of Minnesota; Cheng Tan, Department of Animal Science, University of Minnesota; Yang Da, Department of Animal Science, University of Minnesota

P0366
QTLNetMiner – a Modern Web Application for Network Based Gene-Phenotype Discovery
Keywan Hassani-Pak, Rothamsted Research; Ajit Singh, Rothamsted Research; Christopher Rawlings, Rothamsted Research

P0367
MAGIC BOX – Automated Primer Assay Design for Haploid, Diploid and Polyploid Species
J D Curry, LGC Ltd

P0368
Improving Genome-Specific KASP Markers for Hexaploid Wheat – Application of MAGIC BOX Automated Design Pipeline for Abiotic Stress QTL Dreb1
J D Curry, LGC Ltd

P0369
CrossLink: Genetic Mapping Software for Outbreeding Species
Robert J. Vickerstaff, East Malling Research; Richard J. Harrison, East Malling Research

P0370
CLC Microbiome Genomics Module: Interactive Metagenome Analysis Tools
Mari Miyamoto, QIAGEN K.K.; Arne Materna, QIAGEN Aarhus

P0371
A New Tool for Annotating Locus-Specific Alternate Assemblies and its Application to the Bovine Genome
Colin M. Diesh, Division of Animal Sciences, University of Missouri; Sidharth Sen, MU Informatics Institute, University of Missouri; Darren E. Hagen, Division of Animal Sciences, University of Missouri; Deepak R. Unni, Division of Animal Sciences, University of Missouri; Christine G. Elsik, Division of Animal Sciences, University of Missouri

P0372
Variant Calling in Cats and Humans: Are Human-Based Evaluations of Bioinformatic Tools Sufficient?
Holly C. Beale, Maverix Biomics; Patricia P. Chan, Maverix Biomics; Leslie A. Lyons, University of Missouri-Columbia

P0373
Micro-Syntenies Detected by MicSyn Make It Possible to Show Clearly The Vestige of Ancient WGDs of Plants
Tae-Ho Lee, Genomics Division - National Institute of Agricultural Sciences

P0374
Mix²: An Efficient Software Tool for Accurate Gene Isoform Quantification from RNA-Seq Data
Andreas Tuerk, Lexogen GmbH; Gregor Wiktorin, Lexogen GmbH; Serhat Gueler, Lexogen GmbH

P0375
Mikado: Leveraging Multiple Transcriptome Assembly Methods for Improved Gene Structure Annotation
David Swarbreck, The Genome Analysis Centre

P0376
GMOD in the Cloud 2.0
Scott Cain, Ontario Institute for Cancer Research; Stephen P. Ficklin, Washington State University; Colin Diesh, Division of Animal Sciences, University of Missouri; Lacey-Anne Sanderson, University of Saskatchewan; Lincoln Stein, Ontario Institute of Cancer Research

P0377
Simultaneous Gene Finding in Aligned Genomes
Mario Stanke, University of Greifswald; Stefanie König, University of Greifswald; Lizzy Gerischer, University of Greifswald; Lars Romoth, University of Greifswald

P0378
High-Performance and Complex Information Visualization for Genomic Data
Asher K Haug-Baltzell, University of Arizona; Sean Stephens, University of Arizona; Matthew Bomhoff, University of Arizona; Sean Davey, University of Arizona; Carlos Scheidegger, University of Arizona; Eric Lyons, University of Arizona

P0379
Automated Construction of High-Quality LTR Exemplars from Plant Genomic Sequences
Shujun Ou, Michigan State University; Ning Jiang, Michigan State University

P0380
Semantic Integration of Information Layers in Plant Sciences with the BioXMTM Knowledge Management Environment
Mercedes Ames Sevillano, Biomax Informatics AG; Dieter Maier, Biomax Informatics AG; Sascha Losko, Biomax Informatics AG; Jonathan Sheridan, Biomax Informatics AG

P0381
Improvements to the Flipper Genetic Mapper
Charles F. Crane, USDA-ARS

P0382
TagDigger: User-Friendly Extraction of Read Counts from GBS and RAD-seq Data
Lindsay V. Clark, University of Illinois, Urbana, IL 61801, USA; Erik J. Sacks, Dept of Crop Sciences, University of Illinois

P0383
TreeGenes and CartograTree: Community Resources for Forest Tree Genomics
Steven A Demurjian Jr, University of Connecticut; Emily Grau, Department of Plant Sciences, University of California, Davis; Hans Vasquez-Gross, University of California Davis; Damian Gessler, University of Arizona; David Neale, Dept. Plant Sciences University of California Davis; Jill Wegrzyn, Department of Ecology and Evolutionary Biology, University of Connecticut

P0384
Scalable Functional Classification Pipelines for Phytozome Plant Genes: InterProScan and PMN implemented in Nextflow
Joseph W. Carlson, DOE Joint Genome Institute; David M. Goodstein, DOE Joint Genome Institute; Shengqiang Shu, DOE Joint Genome Institute; Daniel S. Rokhsar, DOE Joint Genome Institute

P0385
Geneious R9: A Bioinformatics Platform for Biologists
Christian Olsen, Biomatters, Inc.; Kashef Qaadri, Biomatters, Inc.; Helen Shearman, Biomatters, Inc.; Richard Moir, Biomatters, Ltd.; Matt Kearse, Biomatters, Ltd.; Sidney Markowitz, Biomatters, Ltd.; Jonas Kuhn, Biomatters, Ltd.; Sebastian Dunn, Biomatters, Ltd.; Alex Cooper, Biomatters, Ltd.

P0386
BIRCH - Seamless Point and Click Data Pipelining for Bioinformatics
Graham Alvare, University of Manitoba; Brian Fristensky, University of Manitoba

P0387
Apollo: Improving Collaborative Genome Curation
Monica C. Munoz-Torres, Lawrence Berkeley National Laboratory; Nathan A Dunn, Lawrence Berkeley National Laboratory; Deepak Unni, Division of Animal Sciences, University of Missouri; Colin Diesh, Division of Animal Sciences, University of Missouri; Christine G. Elsik, Division of Animal Sciences, University of Missouri; Ian Holmes, Department of Bioengineering; Suzanna Lewis, Lawrence Berkeley National Laboratory

P0388
Arabidopsis thaliana Iso-Seq and Gene Annotation
Shengqiang Shu, DOE Joint Genome Institute; Govindarajan Kunde-Ramamoorthy, DOE Joint Genome Institute; Chris Daum, DOE Joint Genome Institute; Chew Yee Ngan, DOE Joint Genome Institute; Chia-Lin Wei, DOE Joint Genome Institute; Jennifer Chiniquy, DOE Joint Genome Institute; Rita Kuo, DOE Joint Genome Institute; Kerrie W. Barry, DOE Joint Genome Institute; David M. Goodstein, DOE Joint Genome Institute; Daniel S. Rokhsar, DOE Joint Genome Institute

P0389
Simplified Access to SRA Genomic Data within GATK
Stephen Sherry, NIH/NLM/NCBI

P1278
The DOE Systems Biology Knowledgebase (KBase): Introduction to a System for Collaborative and Reproducible Inference and Modeling of Biological Function
Robert W. Cottingham, Oak Ridge National Laboratory; Meghan Drake, Oak Ridge National Laboratory; Nomi Harris, Lawrence Berkeley National Laboratory; Sunita Kumari, Cold Spring Harbor Laboratory; Priya Ranjan, Oak Ridge National Laboratory; Samuel M. D. Seaver, Argonne National Laboratory; Doreen Ware, Cold Spring Harbor Laboratory/USDA-ARS; Dave Weston, Oak Ridge National Laboratory; Adam Arkin, Lawrence Berkeley National Laboratory; Sergei Maslov, University of Illinois, Urbana-Champaign; Rick Stevens, Argonne National Laboratory

P1292
iPlantUK: Creating User Friendly RNA-Seq and Mapping by Sequencing Workflows
Ryan Joynson, University of Liverpool

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