MDO3
MICROBIAL GENOMIC ANALYSIS

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Objectives :

Learn to analyze the output of NGS sequencing in order to obtain the most complete genome and be autonomous in the annotation of a bacterial genome.
Understand the differences between several genomes (of the same or different species).

Level of trainees :

Technicians or Engineers  (biologists or bioinformatician).
Knowledge in Bash is a plus for the practical exercises of this training course.

Duration and location:

• Duration : 14 hours over 2 days.
• Location : Soladis training center in Paris or Lyon (to consult the calendar, click on “Sign up”) or directly at your site (minimum of 4 people)

Training fee:

• At Soladis training center : 1150€ tax-free per trainee
• Other : Contact us for an offer adapted to your company.

Soladis invites you to participate in this specialized training module, addressing any biologically oriented public wishing to learn about microbial genomic analysis.

Training Schedule

REMINDER OF THE CONCEPTS ON THE BIOLOGY OF NGS

• The different types of sequencing (1st, 2nd and 3rd generation, paired or single-end)
• Sequencing depth vs. number of samples for reproducibility of analysis
• The different sequenced molecules and their interest

CHOOSE THE CORRECT SEQUENCE ASSEMBLY METHOD

• Mapping vs de novo sequencing
• What are the best tools for bacterial analysis?
• Detection of variations with respect to a reference genome

SEQUENCING DATA PROCESSING

• Quality control
• Read filter

ANNOTATION OF BACTERIAL AND VIRAL GENOMES

• Structural annotation and gene research
• Functional analysis: protein annotation, pattern prediction, functional classifications
• Search for resistance and virulence
• Metabolic reconstruction
• Annotation file standards

COMPARATIVE GENOMICS

• Sequence alignment
• Detection of polymorphisms / Analysis of variants
• Phylogeny
  • Choice of external group
  • Search for homologous sequences
  • Theory on phylogenetic analysis
  • Phylogenetic analysis of samples

APPLICATIONS

• Examples of hands on study cases
• Use of public methods and pipelines (Bash language)

Do not hesitate to contact us for more information about this training, which can be organized in our training center (dates provided on our website) or directly in your premises, according to your preferences.