Program / PROGRAMACIÓN

Day 1. Monday 6 14:30hrsKAWAI, FUJIYOSHI, (ABANTO?)

Lecture 1. (120-min)

• Brief review of introduction to Genomic, Metagenomic and Transcriptomic Analyses
• Amplicon analysis
• From single genes to genomics: genomics
• From single genes to genomics: metagenomics/metagenomic binning
• From single genes to genomics: transcriptomics

Lecture 2. (120-min)

• Statistical mind to find more concrete association with phenomena
• What is your question / How to test your question / Importance of experimental design

Day 2. Tuesday 7 9:00 ÁVILA

Lecture 3. (90-min) AA

• Sequencers, sequencing platform (Illumina, long read)
• Basic data format of basic sequence data (FASTA, GENBANK)
• Basic data format of 'next-generation' sequence (NGS) data (FASTQ)
• Quality information of positions of reads

Lab session 1. (120-min)

Lecture 4. 14:30 (90-min) AA

• Sequence alignment, sequence similarity search

• Two basic approaches, mapping and assembly

Lab session 2. (120-min)

Day 3. Wednesday 8 9:00 KAWAI, LARAMA

MK will send previous material to Giovanni,

Share documents

Practice 1. (120-min) GL

• UNIX basic command, to sniff around sequence files (cd, pwd, ls etc.)
• Examine file contents of MiSeq
• File organization, concept of Path

Practice 2. (120-min) GL

• Text processing (grep, less, tail, head,..)
• To get familiar with NGS sequences #1 (examine NGS sequence files)
• Check contents of fastq

Practice 3. (120-min) MK

• Text processing (wc, cut, sed, awk, redirect (> , » ) etc.), gzip
• To get familiar with NGS sequences #2 (sequential commands by pipe)
• count how many of reads of fastq

Practice 4. (120-min) MK

• Shell script (Batch processing)
• Editor (vim)

Day 4. Thursday 9 9:00 KAWAI, LARAMA

Practice 6. (120-min) GL

• R statistics and graphics language #1

Practice 7. (120-min) GL

• R statistics and graphics language #2
• Goal: * Do (small) analysis and make report of statistical test (apa format)

Lab session 3. (240-min)

Day 5. Friday 10 9:00 KAWAI, LARAMA, ÁVILA

Lecture 6. (120-min) GL

• Quality control of raw sequence data, basic tools for sequence and NGS data

• Commands for NGS analyses
• Commands for sequence analyses
• Brief review of online resources / web services
• NGSToolkit (instead of FastQC)

Practice 8. (120-min)

• To get familiar with NGS sequences #3 (Shell script / make your own pipeline for customanalysisand recordof analysis / screen command)* Sequence similarity search against a genome at hand (Do BLAST search locally)

Lab XX (240-min)

Day 6. Monday 13 9:00 ÁVILA , (LARAMA)

Lecture 7 and Practice 9. (240-min)

• Public sequence database
• Local mirror of databases
• Usage of information of public database
• e.g. Mapping (bowtie2)

Lecture 8 and Practice 10. (240-min)

• Genome assembly

Day 7. Tuesday 15 9:00 KAWAI → tuesday

Lecture 9 and Practice 11. (120-min) MK

* Protein-coding gene prediction, RNA-coding gene prediction, gene annotation → MK

• Muliple sequence alignment
• protein domain search

• Gene contents of genome
• Concept of ortholog
• Concept of conserved single-copy genes

Lecture 10 and Practice 12. (120-min) MK

Lecture 11 and Practice 13. (120-min) MK

Lecture 12 and Practice 14. (120-min) MK

Day 8. Wednsday 16 9:00 - 13:00ABANTO

Lecture 10 and Practice 12. (180-min)

• Introduction of analyses

• Pangenome
• Phylogenetic tree

Day 9. Thursday 17 9:00 KAWAI, LARAMA

• Discuss plans
• groups work
• proposal
• paper introducce
• apply what they learned

git, ask Raphel