Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Long vgp tutorial edits #4542

Merged
merged 29 commits into from
Jan 12, 2024
Merged
Show file tree
Hide file tree
Changes from 27 commits
Commits
Show all changes
29 commits
Select commit Hold shift + click to select a range
86b1460
Long VGP tutorial update
nekrut Nov 21, 2023
7befaf0
fix heading levels
shiltemann Nov 27, 2023
cb5c15f
add border around images per @nekrut's request
shiltemann Nov 27, 2023
b8e2e58
tweak figure layout
shiltemann Nov 27, 2023
81b5488
tweak FAQ layout
shiltemann Nov 27, 2023
0c156d1
move FAQ to tutorial-level FAQ folder
shiltemann Nov 27, 2023
9dd5f85
restore written instructions in FAQ
shiltemann Nov 27, 2023
4d10d79
format FAQ
shiltemann Nov 27, 2023
780fbb7
unify duplicate FAQs
shiltemann Nov 27, 2023
d346a67
rework data upload boxes and FAQs
shiltemann Nov 27, 2023
a5ca087
fix box
shiltemann Nov 27, 2023
f001c0c
fix box
shiltemann Nov 27, 2023
2c9a489
Merge branch 'main' into long_vgp_tutorial_edits
shiltemann Nov 27, 2023
241e33b
Merge branch 'galaxyproject:main' into long_vgp_tutorial_edits
nekrut Nov 28, 2023
91e0b00
further changes
nekrut Nov 28, 2023
e828f33
more changes to hic section
nekrut Nov 29, 2023
c835e09
even more changes to hic section
nekrut Nov 29, 2023
a7bed74
updated busco version and hands-on section
nekrut Nov 30, 2023
f613229
switching to solo mode
nekrut Dec 1, 2023
02c103e
gfastats update for solo
nekrut Dec 1, 2023
473255b
almos done with solo
nekrut Dec 19, 2023
d373e41
replaced salsa with yahs
nekrut Jan 10, 2024
70662e5
additional tweaks
nekrut Jan 10, 2024
5a4d0ae
fixed all tools and figures. reeady for merge
nekrut Jan 11, 2024
d0389bf
removed here links
nekrut Jan 11, 2024
543f15d
one more tweak
nekrut Jan 11, 2024
a708957
fixed snippets spacing
nekrut Jan 11, 2024
e97a09d
fixed anchors
nekrut Jan 11, 2024
32e9c5a
small final changes
bgruening Jan 12, 2024
File filter

Filter by extension

Filter by extension

Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
1 change: 1 addition & 0 deletions topics/assembly/images/vgp_assembly/busco_hap1hap2.svg
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Binary file modified topics/assembly/images/vgp_assembly/merqury_cn_plot.png
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Binary file added topics/assembly/images/vgp_assembly/yahs.png
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
17 changes: 17 additions & 0 deletions topics/assembly/tutorials/vgp_genome_assembly/tutorial.bib
Original file line number Diff line number Diff line change
Expand Up @@ -706,3 +706,20 @@ @article{Korbel2013
title = {Genome assembly and haplotyping with Hi-C},
journal = {Nature Biotechnology}
}

@article{Zhou2022,
author = {Zhou, Chenxi and McCarthy, Shane A and Durbin, Richard},
title = "{YaHS: yet another Hi-C scaffolding tool}",
journal = {Bioinformatics},
doi = {10.1093/bioinformatics/btac808},
volume = {39},
number = {1},
pages = {btac808},
year = {2022},
month = {12},
abstract = "{We present YaHS, a user-friendly command-line tool for the construction of chromosome-scale scaffolds from Hi-C data. It can be run with a single-line command, requires minimal input from users (an assembly file and an alignment file) which is compatible with similar tools and provides assembly results in multiple formats, thereby enabling rapid, robust and scalable construction of high-quality genome assemblies with high accuracy and contiguity.YaHS is implemented in C and licensed under the MIT License. The source code, documentation and tutorial are available at https://github.com/sanger-tol/yahs.Supplementary data are available at Bioinformatics online.}",
issn = {1367-4811},
doi = {10.1093/bioinformatics/btac808},
url = {https://doi.org/10.1093/bioinformatics/btac808},
eprint = {https://academic.oup.com/bioinformatics/article-pdf/39/1/btac808/48763581/btac808.pdf}
}
1,353 changes: 780 additions & 573 deletions topics/assembly/tutorials/vgp_genome_assembly/tutorial.md

Large diffs are not rendered by default.

Loading