PPT-Reference genome assemblies and the technology behind them

Derek M Bickhart Animal Genomics and Improvement Laboratory Research Geneticist Animal derekbickhartarsusdagov Phone 301 5048679 Fax 301 5048092 USDA disclaimer Disclaimers Mention of trade names commercial products or companies in this publication is solely for the purpose of providing specific information and does not imply recommendation or endorsement by the US Department of Agriculture over others not mentioned . School of Engineering. Assembler. Reference. Abyss 1.5.1. Simpson et al., J. T., Wong, K., Jackman, S. D., Schein, J. E., Jones,. . S. J., and . Birol. , I. (2009). Abyss: a parallel assembler for. . Shai. Carmi. Pe’er. lab, Columbia University. and. The Ashkenazi Genome Consortium (TAGC). Boston. September 2013. Outline. Ashkenazi Jewish (AJ) Genetics . and TAGC. Basic Variant Statistics. Utility in AJ Medical . BRIM. Exome. sequencing project. Alexei Fedorov. TOPICS:. Files: . Fastq. , . sam. , bam, . vcf. , bed;. Reference Human Genome;. Transferring files (FTP, SFTP, . wget. ). Input data: “. Fastq. ” files. BIOS 234. June 1. Variant Detection Pipeline. Alignment. Variant Discovery and Genotyping. Prioritization and Filtering. Variant Interpretation. DNA Sequencing. Functional Validation / Clinical Assessment. School of Engineering. Assembler. Reference. Abyss 1.5.1. Simpson et al., J. T., Wong, K., Jackman, S. D., Schein, J. E., Jones,. . S. J., and . Birol. , I. (2009). Abyss: a parallel assembler for. . Outline. What is a “reference genome. ?”. History and examples of . reference-building. When is a reference genome useful. ?. Reference genome assemblies: definition. Database of ordered nucleotides. for. . IRTMTC/ALD. by. IRICEN. BCM ASSEMBLIES . 1. Excavating Chain. Shovel or main link - 82 Nos.. Intermediate link - 82 Nos.. Chain finger - 5 Nos. in each shovel total 410 Nos.. Chain bolt - 2 Nos.. 15, 2021. dsenol@andrew.cmu.edu. . Committee: . Prof. Onur Mutlu (CMU, ETH Zurich). Prof. Saugata Ghose (CMU, UIUC). Prof. James C. Hoe (CMU). Prof. Can Alkan (Bilkent University). and Accurate Assembly Polishing Algorithm. Can Firtina. 1. , Jeremie S. Kim. 1,2. , Mohammed Alser. 1. , . Damla. . Senol. Cali. 2. , A. . Ercument. Cicek. 3. ,. Can Alkan. 3. , and . Onur. Mutlu. G-OnRamp Beta Users Workshop. Wilson Leung. 07/2016. Outline. Obtain genome assemblies from NCBI. Transfer . large genomics datasets to Galaxy. Common bioinformatics file formats . D. atatypes in Galaxy. . https://damlasenolcali.github.io/. . Konstantinos Kanellopoulos, Joel . Lindegger. , Zulal . Bingol. , Gurpreet S. Kalsi, Ziyi Zuo, Can Firtina, Meryem Banu . Cavlak. , Jeremie S. Kim, Nika Mansouri Ghiasi, . “A reference genome (also known as a reference assembly) is a digital nucleic acid sequence database, assembled by scientists as a representative example of a species’ set of genes”. Public databases. assemble. , annotate, and curate the sunflower reference . genome; . integrate . the reference sequence with genetic and physical maps, EST collections, diversity panel sequences, wild species genomes, and QTL and association mapping data; . collection of genome assemblies. Presenter: Hiram Clawson – U.C. Santa Cruz Genomics Institute. hclawson@ucsc.edu. . our work is supported by a number of different grants:. National Human Genome Research Institute U41HG002371.