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
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?
1230 – 1330 Lunch
1330 – 1430 Practical: Using JetStream to analyze data and Linux command line
1430 – 1445 Coffee
1445 – 1700 Practical: Sequence quality control

1700 – 1800

Guest lecture

Tuesday June 27th

1000 – 1100 Introduction to assembly, paired end read technologies, mate pairs, etc
1100 – 1115 Coffee
1115 – 1230 Practical: assembling the reads with spades
1230 – 1330 Lunch
1330 – 1530 Effect of different assemblers and how that changes ecological implications. Chimeras, and other assembly issues. Reconstructing mitochondria from Eukayotes.
1530 – 1545 Coffee
1545 – 1700 Practical: Mapping reads to contigs using bowtie

1700 – 1800

Guest lecture

Wednesday June 28th

1000 – 1100 Why you map reads!
1100 – 1115 Coffee
1115 – 1230 Practical: Visualizing mapped reads: IGV and Anvi’o
1230 – 1330 Lunch
1330 – 1530 crAssphage
1530 – 1545 Coffee
1545 – 1700 Practical: Reconstructing population genomes from mapped reads

1700 – 1800

Guest lecture

Thursday June 29th

1000 – 1100 The Sequence Read Archive and PARTIE
1100 – 1115 Coffee
1115 – 1230 Extracting data from the Sequence Read Archive
1230 – 1330 Lunch
1330 – 1530 Tools for annotation and their implications for downstream analysis
1530 – 1545 Coffee
1545 – 1700 Practical: Annotating with FOCUS, FOCUS2, Super-FOCUS

1700 – 1800

Guest lecture

Friday June 30th

1000 – 1100 How do you know population genomes are correct (checkM, RAST)
1100 – 1115 Coffee
1115 – 1230 Comparison of population genomes and isolate genomes
1230 – 1500 Practical: testing your bins with checkM
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.

There may be a facilities fee for non-SDSU students, post-docs, and faculty to attend the course, and there maybe some fee waivers available.