Short read mapping

• Lecture : basics on read mapping, BAM format, presentation of Bowtie2 (algorithm, parameters)
• Practical session with Bowtie2 and Galaxy: data, exercises

Genome assembly

• Lecture: overlap graphs, De Bruijn graphs, genome assembly in real life

Shotgun metagenomics

• Lecture: the best tools for taxonomic analysis and functional analysis, and the rationale behind those tools
• Practical session with Metaphlan2, One codex, Kaiju, MG-Rast and MGnify (in French)

Algorithms for sequence comparison

This lecture was part of the 2018 Bioinformatics Summer School organized by GDR BIM.

• Lecture: history of alignment methods, seed-based approaches, alignment-free approaches
• Exercises on seeds with errors

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