MDO3
MICROBIAL GENOMIC ANALYSIS
MICROBIAL GENOMIC ANALYSIS
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.
Pedagogical Manager: Agnès ILTIS
“Due to the diversity and specificity of bacterial structures, the processing and analysis of NGS data from bacterial genomes has its own characteristics. Soladis invites you to participate in this training course “Microbial Genomic Analysis” which aims to train you on the use of essential tools for the analysis, annotation and comparison of bacterial genomes. This training, combining theoretical courses and practical exercises, is intended for people wishing to deepen their knowledge of basic microbial genomic analysis.”
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.
Soladis - France (headquarter)
6-8 rue Bellecombe
69006 LYON - FRANCE
Tél: +33(0)4.72.83.86.70
Soladis GmbH - Switzerland
Lange Gasse 15
CH-4052 Basel
Phone: +41(0)58.258.15.80
Soladis Inc. - USA
185 Alewife Brook Pkwy, Unit 210
Cambridge, MA 02138-1100
Phone: (+1)857.675.1189
Contact us
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