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