This is the only on-site training on CLCbio Genomics Workbench in next 12 months, don’t miss it!
Starting the week of Oct. 3, 2016, we will offer free access of the CLC Genomics Workbench Software, along with the Microbial Genomics Module and the Genome Finishing Module, to all USC users.
To help USC researchers get started with this software, QIAGEN will provide an one-day on-site training. Please follow the link below to register for the online training.
CLC Genomics Workbench On-site Training at USC
Date and Time: 10 am to 4 pm, Friday September 30, 2016
Location: Aresty Auditorium, Health Science Campus
Lunch will be provided
10-11 am—Introduction to the CLC Genomics Workbench
• Overview of Application: Reqsequencing, RNA-seq, Small RNA, Epigenomics, De Novo Assembly, Microbial and Metagenomics
• Preprocessing of Data
• Incorporation of MetaData
• Building a workflow/pipeline
• Installation and setting up reference database(s)
11am-noon—DNA-seq, ChIP-seq, and Bisulfite-seq Pipelines
• Map reads to reference
• Indels and structural variants
• Local realignment
• Variant determination
• Annotate, filter and compare variants
• Histone ChIP-seq and bisulfite sequencing
Noon to 1 pm—Lunch will be provided
1:00 pm-2:30 pm—Microbial Module Tools and Metagenomics Pipelines
Microbiome Analysis: Explore the taxonomic and functional composition of Microbial communities
• Analyze 16S rRNA or other amplicon data.
• From raw reads to interactive visualization in four steps.
• De novo or reference based OTU-clustering
• Supports common OTU Databases Greengenes, Silva, and UNITE.
• Analyze and browse micro biome composition at different taxonomic levels and in the context of metadata.
Whole metagenome function analysis: Functional Profiling of Microbiomes
• Assemble whole metagenome datasets
• Functional profiling
• Stacked bar charts, area charts and zoomable sunburst diagrams to explore and compare the functional composition of metagenomic samples, or sample groups.
Typing and whole genome based analysis of microbial isolates
• Confirm the identity of pathogens, or starter cultures.
• Establish an association between an outbreak and its source.
• Monitor pathogens outbreaks.
• Manage samples, meta-information and results all from a convenient Analysis Dashboard.
2:30 pm-3:30 pm—De Novo Assembly and Genome Finishing Tools and Pipelines
• Use reads to assemble an estimate of genome regions
• Support for a variety of data formats, including both short and long reads, and mixing of paired reads
• Assess quality of assembly/QC
• Automate scaffolding, contig joining, and the ordering of contigs relative to each other or to a closely related reference genome
Let us know if you have any questions.
Yibu Chen and Meng Li
Bioinformatics Service Program
Norris Medical Library
University of Southern California