Page Index - davidaray/Genomes-and-Genome-Evolution GitHub Wiki

69 page(s) in this GitHub Wiki:

• Home
• !README: The purpose of these exercises\tutorials
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• 01. Logging In to HPCC and an Intro to Bash and Linux Navigation
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• 02. Working Within the Queue
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• 03. Variables
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• 04. Working with Singularity
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• 05. Let's Talk About Reads and Read Quality
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• 06. Simple Bacterial Genome Assembly
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• 07. Basic Assembly Statistics and Comparing Assemblies
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• 08. Visualizing and Understanding Assembly Graphs
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• 08a. Visualizing and Understanding Assembly Graphs
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• 09. WGS Assembly Using ABYSS
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• 09a. WGS Assembly Using ABYSS
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• 10. Comparing assemblies v2
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• 11. Read Mapping and pileups
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• 12. Estimating Genome Sizes using k mer Counts
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• 13. ABYSS on a C. elegans Genome
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• 14. Genome Annotation with BRAKER
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• 15. Genome Assessment with Compleasm
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• 15. Long Read Genome Assembly with Flye
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• 17. Variant Calling with Freebayes
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• 18. Variant Calling with GATK
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• 19. Identifying TEs in a de novo assembly
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• 20. Masking a genome for TEs
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• Connecting your personal computer
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• Deprecated 13. Long Read Assembly and Polishing
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• Deprecated 00. Getting an HPCC account
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• Deprecated 02. Using Conda
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• Deprecated 05. Let's Talk About Reads and Quality Control
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• Deprecated 06. Simple Bacterial Genome Assembly
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• Deprecated 07. Basic Assembly Statistics and Comparing Assemblies
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• Deprecated 09. WGS Assembly Using ABYSS
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• Deprecated 13. Long Read Assembly with HASLR
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• Deprecated 16. Genome Annotation with Braker
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• Deprecated 17. Calling RADSeq SNPs with Stacks
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