2017 Metagenomics Workshop

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
28
th

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
29
th

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.