Tuesday, September 27, 2016

CLC Genomics Workbench On-Site Training at USC, September 30

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

Training Agenda

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
323-442-3309 (Yibu)
323-442-3447 (Meng)

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