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 (Jonathan Tarn, Valentine Group, UCSB) |
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 (Alyse Larkin, Martiny group, UCI) |
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 | MAGIC blast | RE |
| 1530 – 1545 | Coffee | |
| 1545 – 1700 | Free time | RE |
Thursday June
29th
| 1000 – 1100 | Annotation & crAssphage | RE |
| 1100 – 1115 | Coffee | |
| 1115 – 1230 | Practical: Annotation | RE |
| 1230 – 1330 | Lunch | |
| 1330 – 1530 | Why you map reads! | MH |
| 1530 – 1545 | Coffee | |
| 1545 – 1700 | Practical: Visualizing mapped reads: Anvi’o | MH |
| 1700 – 1800 | Guest lecture – (Megan Morris, Dinsdale group, SDSU) |
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 – 1400 | Practical: testing your bins with checkM | RE |
| 1400 – 1500 | Guest lecture: Samantha Atkinson, Kirby Lab, Medical College of Wisconsin | |
| 1500 – 1800 | BBQ and Social |
Workshop Manual
The manual for the workshop is online. It will be updated during the workshop, but it will always be available at the link above.