Skip to content

linsalrob/ComputationalGenomicsManual

Folders and files

NameName
Last commit message
Last commit date

Latest commit

 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 

Repository files navigation

Edwards Lab DOI License: MIT GitHub language count

ComputationalGenomicsManual

Robs manual for the computational genomics and bioinformatics class

About this manual

Rob, Liz Dinsdale, Tom Jeffries, Bruno Gomez-Gil, Jim Mitchell, and several other colleagues and friends have been teaching genomics and metagenomics for a long time. They have written this manual over the course of several years, and in a variety of formats. Rob moved it to markdown using GitHub in Fall 2018 as part of his computational genomics class.

You can view this manual online

Companion Videos

Companion videos that accompany this class are available on You Tube on Rob's YouTube Playlist.

Chapter Index

Chapter Contents
1. Linux
2. Conda
3. Python
4. Snakemake
5. Sequencing Overview
6. Sequence File Formats
7. Sequence Quality Control
8. Databases
8a. - NCBI Edirect
8b. - NCBI SRA
9. Genome Sequencing Overview
10. Sequence Assembly
11. ORF Calling
12. tRNA and rRNA identification
13. Annotation Pipelines
14. Metagenomics
15. - Example Data Sets
16. Cross Assembly
16a. - Metabat
16b. - CCOM
17. 16S sequencing
18. Host removal
19. FOCUS
20. Kraken
21. SUPER-FOCUS
22. GenomePeek
23. RTMg
24. OrfM and the SEED
25. ANVI'O
26. CheckM

Workshops.

We are using this content in a variety of workshops

Assignments.

Solutions are still not shown, but you can work through some of these

Datasets

We have several different datasets available for you to use to try the course work out. There are both 16S and random metagenomes, and links to genomics data.

PDFs

Note: The PDFs are automatically created from the markdown, and loose some of the images and links. You should probably use the HTML version most of the time.

About Copyright Information

Some of the images used in this manual are currently copyright other people. As noted above, Rob and friends wrote this manual over many years and added the images and cartoons to lighten the manual. We are in the process of identifying the copyright holders and/or identifying images that are not copyrighted. If your rights have been infringed upon, if you would like to provide an indemnification, or if you would like to provide a non-copyrighted image, please contact Rob.

Copyright

This manual is Copyright Robert A. Edwards. 2018.

Citation

If you wish to cite this manual, please cite: Edwards, R. 2018. Computational Genomics. https://linsalrob.github.io/ComputationalGenomicsManual/. Accessed [today's date] DOI: 10.5281/zenodo.7883375

References

We have an extensive list of references available, but if you find something missing that we should have cited (a) we're sorry, we tried to remember all of them and (b) please email Rob or provide a pull request and we'll add it.