cambiotraining/sars-cov-2-genomics

Issues

• add other viruses

  #64 opened 4 months ago
  0

• analysis of co-occurring mutations

  #63 opened 6 months ago
  0

• Make materials consistent throughout

  #62 opened 8 months ago
  0

• Prepare Guacamole instances for Panama workshop

  #61 opened 7 months ago
  0

• update lineage assignment chapter with CLI versions

  #60 opened 8 months ago
  0

• update EQA sample names for UKNEQAS23* panel

  #59 opened 8 months ago
  0

• subsample eqa23 samples from UKHSA

  #58 opened 8 months ago
  1

• switch primer/genome syntax to the more generic `--fasta` and `--bed`?

  #57 opened 8 months ago
  0

• add `mamba activate X` throughout

  #56 opened 8 months ago
  0

• Prepare participants' data shared on dropbox

  #55 opened 7 months ago
  3

• get ground truth mutations for EQA panels '23' version

  #54 opened 8 months ago
  3

• Make appendix documenting all SARS primer schemes

  #53 opened 8 months ago
  1

• Test Guacamole for SARS workshop 5th Feb

  #52 opened 8 months ago
  12

• SARS EQA - 5th Feb

  #51 opened 6 months ago
  0

• ARTIC 5.3.2 - update materials to account for this bug

  #50 opened 8 months ago
  0

• Finishing Instructors' guideline doc before trainers meeting

  #49 opened 8 months ago
  0

• Add workshop page link on the instructor's guideline

  #48 opened 8 months ago
  1

• For instructor guideline documents: Need to address political sensitivities between participants

  #47 opened 8 months ago
  1

• Timetable issue: lengthening software management session time allocation

  #46 opened 8 months ago
  1

• Timetable for Intro to R should be increased to fit the material length

  #45 opened 8 months ago
  0

• Python script to tidy/summarise freyja outputs

  #44 opened 6 months ago
  0

• Prepare data for wastewater materials

  #43 opened 9 months ago
  6

• Learning objectives for new wastewater sections

  #42 opened 6 months ago
  1

• Convert to Quarto template

  #41 opened 8 months ago
  0

• Revise R session

  #40 opened 8 months ago
  1

• Test pipeline on WSL

  #39 opened 8 months ago
  1

• singularity install instructions don't work

  #38 opened 8 months ago
  0

• EQA phylogeny exercise need fixing

  #37 opened 8 months ago
  1

• figtree alternatives

  #36 opened a year ago
  1

• seqkit bug

  #35 opened 8 months ago
  1

• Document primer schemes available

  #34 opened 8 months ago
  1

• Test all the R scripts to make sure they are working properly.

  #33 opened a year ago
  0

• 2023-05 Ghana workshop update

  #32 opened 8 months ago
  1

• New phylogenetics exercise for EQA section

  #31 opened 8 months ago
  2

• Add metagenomic example

  #30 opened 2 years ago
  0

• Documentation about setup

  #29 opened 8 months ago
  0

• Trainer debrief - Singapore workshop

  #28 opened 8 months ago
  1

• where to find the data?

  #27 opened 8 months ago
  7

• add section on CIVET reports

  #25 opened 2 years ago
  1

• Installation script

  #24 opened 2 years ago
  0

• Variants long table CSV - clarifications

  #23 opened 2 years ago
  5

• Pangolin - viralrecon doesn't use most up-to-date version by default

  #22 opened 8 months ago
  1

• Add note about mixed bases

  #21 opened 2 years ago
  0

• Unix - improvements to exercises

  #20 opened 8 months ago
  1

• Which variants are used in consensus assembly?

  #19 opened 2 years ago
  2

• details about recombinant lineage classification

  #18 opened 2 years ago
  0

• mistakes in consensus exercise solution

  #17 opened 2 years ago
  0

• pipeline cheatsheet

  #16 opened 2 years ago
  1

• expanded materials - ideas

  #15 opened 2 years ago
  0

• expland explanation on amplicon vs metagenomic

  #14 opened 2 years ago
  0