From e7ff06c61533c5edd092ea88cf4ed1cdbe6e9953 Mon Sep 17 00:00:00 2001 From: Anna Syme Date: Thu, 14 Sep 2023 14:17:24 +1000 Subject: [PATCH] Update vgp-workflows.md Format web links --- webapp/home/templates/home/pages/vgp-workflows.md | 15 ++++++++------- 1 file changed, 8 insertions(+), 7 deletions(-) diff --git a/webapp/home/templates/home/pages/vgp-workflows.md b/webapp/home/templates/home/pages/vgp-workflows.md index c482bfc6..448525ef 100644 --- a/webapp/home/templates/home/pages/vgp-workflows.md +++ b/webapp/home/templates/home/pages/vgp-workflows.md @@ -5,9 +5,9 @@ Anna Syme ## What are the VGP workflows? * These are workflows for genome assembly, developed for the Vertebrate Genome Project -* Website: https://vertebrategenomesproject.org/ -* Data at Genome Ark https://vgp.github.io/genomeark/ -* Paper: Rhie, A., McCarthy, S.A., Fedrigo, O. et al. Towards complete and error-free genome assemblies of all vertebrate species. Nature 592, 737–746 (2021). https://doi.org/10.1038/s41586-021-03451-0 +* Website: [https://vertebrategenomesproject.org/](https://vertebrategenomesproject.org/) +* Data at Genome Ark [https://vgp.github.io/genomeark/](https://vgp.github.io/genomeark/) +* Paper: [Rhie, A., McCarthy, S.A., Fedrigo, O. et al. Towards complete and error-free genome assemblies of all vertebrate species. Nature 592, 737–746 (2021).](https://doi.org/10.1038/s41586-021-03451-0) * This paper covers the testing of tools and workflows. We recommend also looking at the Supplementary Information which is very informative. ## Are the VGP workflows in Galaxy Australia? @@ -33,6 +33,7 @@ Anna Syme ## What data do I need? Overall, you need these inputs: + * HiFi reads as collection * If HiFi data in BAM format, convert to FASTQ using the BAM to FASTQ + QC v1.0 workflow * then group output FASTQ files into a single collection @@ -66,10 +67,10 @@ For each of the other workflows, you will need these inputs: ## Do I need any background knowledge before I run these workflows? * We recommend the Galaxy Training Network tutorials. -* Introduction to Galaxy: https://training.galaxyproject.org/training-material/topics/introduction/tutorials/galaxy-intro-short/tutorial.html -* Assembly: https://training.galaxyproject.org/training-material/topics/assembly/tutorials/general-introduction/tutorial.html -* QC: https://training.galaxyproject.org/training-material/topics/sequence-analysis/tutorials/quality-control/tutorial.html -* VGP: https://training.galaxyproject.org/training-material/topics/assembly/tutorials/vgp_genome_assembly/tutorial.html +* [Introduction to Galaxy](https://training.galaxyproject.org/training-material/topics/introduction/tutorials/galaxy-intro-short/tutorial.html) +* [Assembly](https://training.galaxyproject.org/training-material/topics/assembly/tutorials/general-introduction/tutorial.html) +* [QC](https://training.galaxyproject.org/training-material/topics/sequence-analysis/tutorials/quality-control/tutorial.html) +* [VGP tutorials](https://training.galaxyproject.org/training-material/topics/assembly/tutorials/vgp_genome_assembly/tutorial.html) * These should be enough to get you started running the VGP workflows, but there are many additional tutorials that would also be useful. * As most species have never had their genome sequenced, it is not possible to guarantee existing workflows are optimal for new data. * It is most likely that any new genome assembly will have its own set of required workflow and analysis customisations to account for things such as ploidy and repeats.