Day 1: Assembly computation

October 5th

Description

In this session, the participants will familiarize with the raw long reads, learn how to assemble genomic reads, how to map genomic and RNA-seq reads to a reference genome, and finally how to proceed to transcriptome assembly.

Approximate schedule

• 14:00 - 14:30 --- Daniel: General introduction, experimental design.
• 14:30 - 15:00 --- Kamil: HDF archives for raw data, reads extraction.
• 15:00 - 15:15 --- Coffee break.
• 15:15 - 16:00 --- Kamil: Genome assembly.
• 16:00 - 16:15 --- Coffee break.
• 16:15 - 17:15 --- Amina: Transcriptome assembly.
• 17:15 - 17:30 --- Daniel: Overview of Day 1.

Day2: Downstream analysis

October 6th

Description

In this session, the participants will interpret assemblies they have computed on the first day, learning how to assess quality of a genome assembly and run downstream analysis.

Approximate schedule

• 09:00 - 09:15 --- Daniel: reminder of Day 1, general introduction to Day 2.
• 09:15 - 10:00 --- Kamil: Assessing quality of genome assembly.
• 10:00 - 10:15 --- Coffee break.
• 10:15 - 11:00 --- Amina: Post-transcriptome assembly steps.
• 11:00 - 11:15 --- Coffee break.
• 11:15 - 12:15 --- Daniel: Post-genome assembly steps.
• 12:15 - 12:30 --- Everybody: General overview.

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