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License: MIT License
Phylogenomic analysis on the CIPRES REST portal
License: MIT License
The hackathon preprint will be submitted to BioHackrxiv and will be based on the manuscript template in doc/paper.md
Once all the individual steps (e.g. #3, #4) are working and are orchestrated using CWL (#5), an essential step for redistribution is that the Docker container does not have to be rebuilt by other users but can just be pulled down by the cwl-runner
. For this to work, the container should be pushed to Docker hub. This will likely result in a tag that matches the name of this repo, i.e. naturalis/covid19-phylogeny
under the docker hub naturalis organization
The experiences detailed here (nextstrain/ncov#268) show that doing the MSA in one big run eventually becomes prohibitive. This was not a problem for the 400 GenBank genomes set, but as those submissions are increasing (or when we add GISAID data) it becomes an issue.
MAFFT has the virtue of being the standard that is now being used (e.g. by Rambaut et al.) but it might be slower than Muscle (@rvosa's subjective experience)? Both can be run on the CIPRES cluster. Test and decide.
Release the cipresrun REST client as a bioconda package
Please specify more to add onto Documentation.md
The goal of the basic workflow is to be able to consume unaligned FASTA, align this (i.e. solve #3) and build a tree with it (by addressing #4). These steps are implemented with tools, scripts, and web service calls that are all provisioned inside a Docker container (whose Dockerfile is in the root of the repo, and whose tag will be the same as the repo name).
Subsequently, these steps will be chained together using CWL, most of which is already scaffolded in PR #1. The essential test is therefore that we should be able to run the whole thing on a clean computer using something like cwl-runner
. We will then submit this to covid19.workflowhub.eu.
i.e. rewrite requests to LWP::UserAgent
IQTree is more or less the standard for building trees from viral genomes. A somewhat costly step that it does by default is to do full model testing to decide on the right model. Perhaps as per Rambaut et al. we might just settle on HKY85+G
.
For the clade assignments, bootstrap support would be good (e.g. 1000 replicates), so experiment with how costly that is (-bnni
parameter, I think).
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