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mestato
EPP622_2026

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Module 2

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Meg Staton edited this page Sep 9, 2026 · 13 revisions

TBD

Wiki pages Pages 33

Home
AI generated overview of SNP Calling
BLAST and DIAMOND Lab
Class 2 Discussion Seeds
Class 4 Discussion Seeds
Class 5 Discussion Seeds
Day 10 discussion seeds
Discussion prompts for long read sequencing overview papers
Fix conda speed issue (hopefully)
ISAAC intro
ISAAC topic request list
Long Read QC and mapping with slurm!
Long Read SV calling and JBrowse viewing
Meet Your Classmates
Module 1
Module 2
Module 2.1 project set up, conda, fastqc, multiqc
Module 2.2 bwa mem, samtools
Module 2.2 fastp
Module 2.2 fastp, bwa mem, samtools
Module 2.3 bwa mem2
Module 2.3 bcftools, vcf filtering
Module 2.4 bcftools and vcf filtering
Module 2.5 JBrowse2 and Variant Statistic Plots
Module 2.6 SnpEff, Combining VCFs, and SNP Ordination
SVs impacting genes
Test 1 Option 2 Practice Test
Test 1 Options
Test 2 Description
Test 2 Wiki template raw
Test 2 Wiki template rendered
Test 2: A celebration of your new SNP calling expertise
the basics of BLAST and DIAMOND

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