Page Index - mestato/EPP622_2026 GitHub Wiki
88 page(s) in this GitHub Wiki:
- Home
- Login Options
- Module 1: Command Line Mastery 8/18-9/8
- Module 2: Short Read Variation 9/10-10/1
- Module 2 Grading
- Class 8. Thursday September 10th
- Class 9. Tuesday September 15th
- Class 10. Thursday September 17th
- Class 11. Tuesday September 22nd
- Class 12. Thursday September 24th
- Class 13. Tuesday September 29th
- Class 14. Thursday October 1st
- Class 15. Thursday October 8th
- Test 2
- Module 3: Long Read Assembly and Structural Variation 10/15-11/5
- Module 3 Grading
- Class 16. Tuesday October 13th
- Class 17. Thursday October 15th
- Class 18. Tuesday October 20th
- Class 19. Thursday October 22nd
- Class 20. Tuesday October 27th
- Class 21. Thursday October 29th
- NO CLASS. Tuesday November 3rd
- Class 21. Thursday November 5th
- Class 22. Tuesday November 10th
- Module 4: Choose your own adventure 11/5-12/1
- AI generated overview of SNP Calling
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- BLAST and DIAMOND Lab
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- Class 2 Discussion Seeds
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- Class 4 Discussion Seeds
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- Class 5 Discussion Seeds
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- Day 10 discussion seeds
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- Discussion prompts for long read sequencing overview papers
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- Fix conda speed issue (hopefully)
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- ISAAC intro
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- ISAAC topic request list
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- Long Read QC and mapping with slurm!
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- Long Read SV calling and JBrowse viewing
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- Meet Your Classmates
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- Module 1
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- Module 2
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- Module 2.1 project set up, conda, fastqc, multiqc
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- Module 2.2 bwa mem, samtools
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- Module 2.2 fastp
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- Module 2.2 fastp, bwa mem, samtools
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- Module 2.3 bwa mem2
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- Module 2.3 bcftools, vcf filtering
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- Module 2.4 bcftools and vcf filtering
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- Module 2.5 JBrowse2 and Variant Statistic Plots
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- Module 2.6 SnpEff, Combining VCFs, and SNP Ordination
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- Test 1 Option 2 Practice Test
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- Test 1 Options
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- Test 2 Description
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- Test 2 Wiki template raw
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- Test 2 Wiki template rendered
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- Test 2: A celebration of your new SNP calling expertise
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- the basics of BLAST and DIAMOND
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