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| <!-- | ||
| #--- | ||
| #layout: lesson | ||
| #root: . | ||
| #permalink: index.html # Is the only page that don't follow the partner /:path/index.html | ||
| #--- | ||
| #The lessons of the first two days use the | ||
| #[Software Carpentry]({{ site.swc_site }}) and | ||
| #[Data Carpentry]({{ site.dc_site }}) lesson template and are based on the [Data Carpentry Genomics lesson]({{ site.dc_site #}}). | ||
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| #> ## Schedule week 1: Prokaryotic microbes (bacteria) | ||
| #> | ||
| #> Days 1-2 are taught by Anita Schuerch. Days 3-4 are taught by Aldert Zomer and Bas Dutilh. | ||
| #> | ||
| #> 1. Tuesday, 3 April: Intro to data and the command line, shell scripting, Quality control, workflows | ||
| #> 2. Wednesday, 4 April: Workflows continued, Genome visualization, Metadata manipulation with R | ||
| #> 3. Thursday, 5 April: Trimming, QC, Assembly, Assembly lecture | ||
| #> 4. Friday, 6 April: Annotation, pangenome analysis, Association scoring, Wrap-up | ||
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| #> ## Schedule week 2: Eukaryotic microbes (fungi) | ||
| #> | ||
| ##> Days 5-8 are taught by Jerome Collemare, Ronnie de Jonge, and Robin Ohm. | ||
| #> | ||
| #> 5. Monday, 9 April: Assembly | ||
| #> 6. Tuesday, 10 April: RNAseq and gene prediction | ||
| #> 7. Wednesday, 11 April: Functional annotation | ||
| #> 8. Thursday, 12 April: Comparative genomics | ||
| #> 9. Friday, 13 April: Exam | ||
|
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||
| #> ## Data | ||
| #> | ||
| #> In days 1-2 we will use data from a long term evolution experiment published in 2012: [Genomic analysis of a key #innovation in an experimental Escherichia coli population by Blount ZD, Barrick JE, Davidson CJ, and Lenski RE. (doi: #10.1038/nature11514)](https://www.nature.com/articles/nature11514). | ||
| #> | ||
| #> We are using [this](http://pad.software-carpentry.org/2018-04-03-Utrecht) collaborative document. | ||
| #> | ||
| #> The etherpad of Day 1 is archived [here](files/2018-04-03-Utrecht-Day1.pdf). | ||
| #> The etherpad of Day 2 is archived [here](files/2018-04-03-Utrecht-Day2.pdf). | ||
| #{: .prereq} | ||
| The lessons of the first two days use the | ||
| [Software Carpentry]({{ site.swc_site }}) and | ||
| [Data Carpentry]({{ site.dc_site }}) lesson template and are based on the [Data Carpentry Genomics lesson]({{ site.dc_site }}). | ||
| > ## Schedule week 1: Prokaryotic microbes (bacteria) | ||
| > | ||
| > Days 1-2 are taught by Anita Schuerch. Days 3-4 are taught by Aldert Zomer and Bas Dutilh. | ||
| > | ||
| > 1. Tuesday, 3 April: Intro to data and the command line, shell scripting, Quality control, workflows | ||
| > 2. Wednesday, 4 April: Workflows continued, Genome visualization, Metadata manipulation with R | ||
| > 3. Thursday, 5 April: Trimming, QC, Assembly, Assembly lecture | ||
| > 4. Friday, 6 April: Annotation, pangenome analysis, Association scoring, Wrap-up | ||
| > ## Schedule week 2: Eukaryotic microbes (fungi) | ||
| > | ||
| > Days 5-8 are taught by Jerome Collemare, Ronnie de Jonge, and Robin Ohm. | ||
| > | ||
| > 5. Monday, 9 April: Assembly | ||
| > 6. Tuesday, 10 April: RNAseq and gene prediction | ||
| > 7. Wednesday, 11 April: Functional annotation | ||
| > 8. Thursday, 12 April: Comparative genomics | ||
| > 9. Friday, 13 April: Exam | ||
| > ## Data | ||
| > | ||
| > In days 1-2 we will use data from a long term evolution experiment published in 2012: [Genomic analysis of a key innovation in an experimental Escherichia coli population by Blount ZD, Barrick JE, Davidson CJ, and Lenski RE. (doi: 10.1038/nature11514)](https://www.nature.com/articles/nature11514). | ||
| > | ||
| > We are using [this](http://pad.software-carpentry.org/2018-04-03-Utrecht) collaborative document. | ||
| > | ||
| > The etherpad of Day 1 is archived [here](files/2018-04-03-Utrecht-Day1.pdf). | ||
| > The etherpad of Day 2 is archived [here](files/2018-04-03-Utrecht-Day2.pdf). | ||
| {: .prereq} | ||
| In week 2 we will use publically available genome and RNA data from the organism Zymoseptoria tritici and related fungi. Outline and instructions (to be made available at the start of week 2) can be found here: | ||
| https://drive.google.com/drive/folders/1_iTtzbKqk7j5uzMeN1R_lFgPGuF6KURl?usp=sharing | ||
| {% include links.md %} | ||
| --> |