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ComputationalGenomicsManual

Robs manual for the computational genomics and bioinformatics class.

Edwards Lab

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

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]

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.