Friday September 30th, 2016
10:00am – 11:00am: 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)
11:00am – 12:00pm: 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
12:00pm – 1:00pm: Lunch (provided)
1:00pm – 2:30pm: 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.
2:30pm – 3:30pm: 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