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Bioinformatics Software: CLC Genomics Workbench

General Information

NML Bioinformatics is very pleased to host a one-day training event for CLC Genomics Workbench and the Microbial Modules.

Major Topics:

  • DNA-seq Analysis and Epigenomics (ChIP-seq) Pipelines
    • Reads mapping
    • Variant calling
    • Histone ChIP-seq and bisulfite sequencing
  • Microbial Module Tools and Pipelines
    • Microbial communities analysis (16S rRNA and other amplicon data)
    • Whole metagenome functional profiling (assembly, functional profiling) 
  • De novo Assembly and Genome Finishing Tools and Pipelines
    • Genome assembly
    • Scaffolding, contig joining

Time: September 30, 2016

Place: Aresty Auditorium, HSC

Registration is mandatory. 

Training Agenda

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