cambiotraining sars-cov-2-genomics issues

cambiotraining / sars-cov-2-genomics

Course materials for an introduction to SARS-CoV-2 sequencing data analysis

http://cambiotraining.github.io/sars-cov-2-genomics/

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add other viruses

#64 tavareshugo opened 4 weeks ago
0
analysis of co-occurring mutations

#63 tavareshugo opened 2 months ago
0
Make materials consistent throughout

#62 tavareshugo opened 4 months ago
0
Prepare Guacamole instances for Panama workshop

#61 tavareshugo closed 3 months ago
0
update lineage assignment chapter with CLI versions

#60 tavareshugo closed 4 months ago
0
update EQA sample names for UKNEQAS23* panel

#59 tavareshugo closed 4 months ago
0
subsample eqa23 samples from UKHSA

#58 tavareshugo closed 4 months ago
1
switch primer/genome syntax to the more generic `--fasta` and `--bed`?

#57 tavareshugo opened 4 months ago
0
add `mamba activate X` throughout

#56 tavareshugo opened 4 months ago
0
Prepare participants' data shared on dropbox

#55 tavareshugo closed 3 months ago
3
get ground truth mutations for EQA panels '23' version

#54 tavareshugo closed 4 months ago
3
Make appendix documenting all SARS primer schemes

#53 tavareshugo closed 4 months ago
1
Test Guacamole for SARS workshop 5th Feb

#52 tavareshugo closed 4 months ago
12
SARS EQA - 5th Feb

#51 tavareshugo closed 2 months ago
0
ARTIC 5.3.2 - update materials to account for this bug

#50 tavareshugo closed 4 months ago
0
Finishing Instructors' guideline doc before trainers meeting

#49 bsalehe closed 4 months ago
0
Add workshop page link on the instructor's guideline

#48 bsalehe closed 4 months ago
1
For instructor guideline documents: Need to address political sensitivities between participants

#47 bsalehe closed 4 months ago
1
Timetable issue: lengthening software management session time allocation

#46 bsalehe closed 4 months ago
1
Timetable for Intro to R should be increased to fit the material length

#45 bsalehe closed 4 months ago
0
Python script to tidy/summarise freyja outputs

#44 tavareshugo closed 2 months ago
0
Prepare data for wastewater materials

#43 tavareshugo opened 5 months ago
6
Learning objectives for new wastewater sections

#42 tavareshugo closed 2 months ago
1
Convert to Quarto template

#41 tavareshugo closed 4 months ago
0
Revise R session

#40 tavareshugo closed 4 months ago
1
Test pipeline on WSL

#39 tavareshugo closed 4 months ago
1
singularity install instructions don't work

#38 tavareshugo closed 4 months ago
0
EQA phylogeny exercise need fixing

#37 tavareshugo closed 4 months ago
1
figtree alternatives

#36 tavareshugo opened 1 year ago
1
seqkit bug

#35 tavareshugo closed 4 months ago
1
Document primer schemes available

#34 tavareshugo closed 4 months ago
1
Test all the R scripts to make sure they are working properly.

#33 bsalehe closed 1 year ago
0
2023-05 Ghana workshop update

#32 tavareshugo closed 4 months ago
1
New phylogenetics exercise for EQA section

#31 tavareshugo closed 4 months ago
2
Add metagenomic example

#30 tavareshugo opened 1 year ago
0
Documentation about setup

#29 tavareshugo closed 4 months ago
0
Trainer debrief - Singapore workshop

#28 tavareshugo closed 4 months ago
1
where to find the data?

#27 liamxg closed 4 months ago
7
typo correction

#26 Sam-Sims closed 1 year ago
0
add section on CIVET reports

#25 tavareshugo opened 1 year ago
1
Installation script

#24 tavareshugo closed 1 year ago
0
Variants long table CSV - clarifications

#23 tavareshugo opened 1 year ago
5
Pangolin - viralrecon doesn't use most up-to-date version by default

#22 tavareshugo closed 4 months ago
1
Add note about mixed bases

#21 tavareshugo opened 1 year ago
0
Unix - improvements to exercises

#20 tavareshugo closed 4 months ago
1
Which variants are used in consensus assembly?

#19 tavareshugo opened 1 year ago
2
details about recombinant lineage classification

#18 tavareshugo opened 1 year ago
0
mistakes in consensus exercise solution

#17 tavareshugo closed 1 year ago
0
pipeline cheatsheet

#16 tavareshugo opened 2 years ago
1
expanded materials - ideas

#15 tavareshugo opened 2 years ago
0