Once again we are offering a one week workshop on metagenomics data analysis at San Diego State University from June 26th to June 30th. The course will have a focus on random metagenomics sequencing and data analysis (not 16S sequencing). The course will cover sequencing technologies and sequencing approaches, data analysis using the linux command line, paired end sequencing, sequence assembly, mapping reads and visualization, population genomics, and extracting data from the sequence read archive. If you are interested, click the read more.
We are still finalizing the speakers and syllabus for the course, but this is the draft agenda:
Monday June 26th
| 1000 – 1100 | Introduction to metagenomics. What can we do with metagenomics, 16S vs. random sequencing. Sampling strategies and sample sizes |
ED |
| 1100 – 1115 | Coffee | |
| 1115 – 1230 | Different sequencing technologies library preps, how much DNA do you need, sequencing protocols; Sequencing class results; What do sequences look like? |
ED |
| 1230 – 1330 | Lunch | |
| 1330 – 1430 | Practical: Using JetStream to analyze data and Linux command line |
RE |
| 1430 – 1445 | Coffee | |
| 1445 – 1700 | Practical: Sequence quality control | RE |
| 1700 – 1800 | Guest lecture (Valentine student) |
Tuesday June 27th
| 1000 – 1100 | QIIME and Unifrac | SK |
| 1100 – 1115 | Coffee | |
| 1115 – 1230 | QIIME and Unifrac | SK |
| 1230 – 1330 | Lunch | |
| 1330 – 1530 | Effect of different assemblers and how that changes ecological implications. Chimeras, and other assembly issues. Sequence profiling and phylogenetics. |
ED |
| 1530 – 1545 | Coffee | |
| 1545 – 1700 | Practical: Mapping reads to contigs using bowtie | RE |
| 1700 – 1800 | Guest lecture (Martiny student) |
Wednesday June
28th
| 1000 – 1100 | The Sequence Read Archive and NCBI | BB |
| 1100 – 1115 | Coffee | |
| 1115 – 1230 | Extracting data from the Sequence Read Archive | BB |
| 1230 – 1330 | Lunch | |
| 1330 – 1530 | Tools for annotation and their implications for downstream analysis |
RE |
| 1530 – 1545 | Coffee | |
| 1545 – 1700 | Practical: Annotating with FOCUS, FOCUS2, Super-FOCUS | RE |
| 1700 – 1800 | Guest lecture – Megan Morris |
Thursday June
29th
| 1000 – 1100 | crAssphage | RE |
| 1100 – 1115 | Coffee | |
| 1115 – 1230 | Practical: Reconstructing population genomes from mapped reads | RE |
| 1230 – 1330 | Lunch | |
| 1330 – 1530 | Why you map reads! | ED |
| 1530 – 1545 | Coffee | |
| 1545 – 1700 | Practical: Visualizing mapped reads: IGV and Anvi’o | ED |
| 1700 – 1800 | Guest lecture |
Friday June 30th
| 1000 – 1100 | How do you know population genomes are correct (checkM, RAST) | RE |
| 1100 – 1115 | Coffee | |
| 1115 – 1230 | Comparison of population genomes and isolate genomes | ED |
| 1230 – 1500 | Practical: testing your bins with checkM | RE |
| 1500 – 1800 | BBQ and Social |
If you are interested in more information about the course please complete this form. It does not guarantee a reservation for the course, but we will try and accommodate everyone that applies.