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ANDNMO12
Analysis of NGS Data from Non-Model OrganismsCo-organised by Gabriel Marais, Raquel Tavares and Pedro Fernandes Course Timetable |
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Mon, June 4th |
NGS technologies and data processing
Day #1
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| 09:00-09:30 Organisers and Instructors |
General introduction to the course. Objectives of the course, presentation of the speakers, the plan, practical details, presentation of the students, etc. |
| 09:30-11:00 Ludovic Orlando |
Available Next Generation Sequencing technologies and forthcoming ones. Principles, data produced, sequencing errors, costs, etc. |
| 11:00-11:30 | Coffee Break | 11:30-12:30 Ludovic Orlando |
Available Next Generation Sequencing technologies (continued). |
| 12:30-14:00 | Lunch Break |
| 14:00-15:00 |
Research seminar by Ludovic Orlando Ancient DNA: from molecules to genomes and population dynamics |
15:00-16:00 Ludovic Orlando |
Processing NGS reads: from raw sequence data to SNP calling using command line statements in Linux Read quality control, trimming, mapping, SNP variant calling, single-end versus paired-end reads |
| 16:00-16:30 | Tea Break |
| 16:30-18:00 Ludovic Orlando |
Processing NGS reads: from raw sequence data to SNP calling using command line statements in Linux Read quality control, trimming, mapping, SNP variant calling, single-end versus paired-end reads (continued) |
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Tue, June 5th |
De novo genome assembly and analysis
Day #2
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| 09:00-10:00 Ludovic Orlando |
Wrap-up session on the previous day's work |
| 10:00-11:00 Ed Green |
Examples of NGS genome projects, methods for processing, assembling and annotating genomes, methodological challenges, examples of evolutionary genomics analysis. |
| 11:00-11:30 | Coffee Break |
| 11:30-12:30 Ed Green |
Examples of NGS genome projects, methods for processing, assembling and annotating genomes, methodological challenges, examples of evolutionary genomics analysis. (continued) |
| 12:30-14:00 | Lunch Break |
| 14:00-15:00 |
Research seminar by Ed Green Recent human evolution as revealed by ancient hominins |
| 15:00-16:00 Ed Green |
Tools for genome assembly |
| 16:00-16:30 | Tea Break |
| 16:30-18:00 | Genome assembly quality control |
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Wed, Jun 6th |
Transcriptome-based population genomics with NGS
Day #3
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| 09:00-10:00 Ed Green |
Wrap-up session on the previous day's work |
| 10:00-11:00 Nicolas Galtier |
Examples of NGS transcriptome projects, methods for processing, assembling and annotating transcriptomes, methodological challenges, examples of population genomics analysis using transcriptomes. |
| 11:00-11:30 | Coffee Break |
| 11:30-12:30 Nicolas Galtier |
Examples of NGS transcriptome projects, methods for processing, assembling and annotating transcriptomes, methodological challenges, examples of population genomics analysis using transcriptomes. (continued) |
| 12:30-14:00 | Lunch Break |
| 14:00-15:00 |
Research seminar by Nicolas Galtier Species life-history traits and genome evolution |
| 15:00-16:30 João Lourenço |
Processing, assembly, mapping and SNP calling of transcriptomic data using the Galaxy framework |
| 16:00-16:30 | Tea Break |
| 16:30-17:00 João Lourenço |
Processing, assembly, mapping and SNP calling of transcriptomic data using the Galaxy framework (continued) |
| 17:00-18:00 All |
Final Wrap-up session. |
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Notes:
- The three research seminars (blue) will be held in an auditorium and open to the public. - There will be an optional course dinner in Oeiras, open to participants, teachers and organizers. |
| Course Homepage |
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Instituto Gulbenkian de Ciência, Apartado 14, 2781-901 Oeiras, Portugal Last updated: April 10th 2012 |