Submitting a New Hybrid Genome Assembly Tutorial #6389
Conversation
|
@nekrut and @Delphine-L I just wanted to check if there is anything that you need me to do before this can be reviewed? Thanks. |
There was a problem hiding this comment.
@GraceAHall finally :) Happy to find a bit of time for this, for a mate.
Overall it looks very good @tflowers15, good formatting, good use of boxes, my comments are mostly stylistic + accessibility.
| > {: .solution} | ||
| > | ||
| {: .question} | ||
|
|
There was a problem hiding this comment.
Would including bandage here be instructive for the learners?
There was a problem hiding this comment.
I did consider including a step on running bandage to view the assembly graph, however I don't think it provides much insight. I would prefer to not include it when I run local workshops using this tutorial. This tutorial is based on the workshops that I run at The University of Melbourne.
Sorry, I got a bit delayed, I should be done with my review today |
| # Conclusion | ||
|
|
||
| We have covered two methods for hybrid de novo assembly. The combination of long- and short-read technology is clearly powerful, represented by our ability to create a good assembly with only 25x coverage (100Mb) of Nanopore and 50x coverage (200Mb) of Illumina reads. | ||
|
|
There was a problem hiding this comment.
Do you have recommendations on the minimum coverage to get a good quality genome ? and what would be good quality metrics if you don't have a reference ?
There was a problem hiding this comment.
I have spent some time investigating sequencing coverage to get a good quality genome and I have not found any clear answer and I think it is better to not provide a recommendation. I have added a paragraph to the conclusion addressing quality metrics when there is no reference genome.
Co-authored-by: Helena <[email protected]>
Co-authored-by: Helena <[email protected]>
|
@hexylena and @Delphine-L Thank you both for your comments and edits. I have addressed all of them and either accepted the proposed commit, updated the tutorial as suggested or replied to your comment when I have not fully implemented the suggested change (2 suggestions). |
3 participants
I am submitting a new tutorial on performing hybrid genome assembly using Galaxy. This tutorial is based on a tutorial created by Melbourne Bioinformatics.
This pull request includes the tutorial markdown file and tutorial images and an associated workflow and workflow tests. The CONTRIBUTORS.yaml file has also been updated to include new details for one of the co-authors of the tutorial. All datasets used in this tutorial are available in a published zenodo repository.
I confirm that all images are allowed to be re-hosted by the GTN.