diff --git a/README.md b/README.md index e8433e5a..d39ffabc 100644 --- a/README.md +++ b/README.md @@ -5,8 +5,8 @@ This is the [Nextstrain](https://nextstrain.org) build for dengue, visible at The build encompasses fetching data, preparing it for analysis, doing quality control, performing analyses, and saving the results in a format suitable for -visualization (with [auspice][]). This involves running components of -Nextstrain such as [fauna][] and [augur][]. +visualization (with [auspice][]). These steps involves running +[augur][] subcommands. All dengue-specific steps and functionality for the Nextstrain pipeline should be housed in this repository. @@ -15,19 +15,16 @@ housed in this repository. ## Usage +See the [Installing Nextstrain guide][] for how to install the `nextstrain` command. + If you're unfamiliar with Nextstrain builds, you may want to follow our -[quickstart guide][] first and then come back here. +[Running a Pathogen Workflow guide][] first and then come back here. The easiest way to run this pathogen build is using the Nextstrain command-line tool: nextstrain build . -See the [nextstrain-cli README][nextstrain-cli] for how to install the `nextstrain` command. - -Alternatively, you should be able to [run the build using `snakemake` within a -suitably-configured local environment][nextstrain-snakemake]. - Build output goes into the directories `data/`, `results/` and `auspice/`. Once you've run the build, you can view the results in auspice: @@ -42,12 +39,26 @@ specifies its file inputs and output and also its parameters. There is little re rule should be able to be reasoned with on its own. -### fauna / RethinkDB credentials +### Using GenBank data + +This build starts by pulling preprocessed sequence and metadata files from: + +* https://data.nextstrain.org/files/dengue/sequences_all.fasta.zst +* https://data.nextstrain.org/files/dengue/metadata_all.tsv.zst +* https://data.nextstrain.org/files/dengue/sequences_denv1.fasta.zst +* https://data.nextstrain.org/files/dengue/metadata_denv1.tsv.zst +* https://data.nextstrain.org/files/dengue/sequences_denv2.fasta.zst +* https://data.nextstrain.org/files/dengue/metadata_denv2.tsv.zst +* https://data.nextstrain.org/files/dengue/sequences_denv3.fasta.zst +* https://data.nextstrain.org/files/dengue/metadata_denv3.tsv.zst +* https://data.nextstrain.org/files/dengue/sequences_denv4.fasta.zst +* https://data.nextstrain.org/files/dengue/metadata_denv4.tsv.zst + +The above datasets have been preprocessed and cleaned from GenBank and are updated at regular intervals. -This build starts by pulling sequences from our live [fauna][] database (a RethinkDB instance). This -requires environment variables `RETHINK_HOST` and `RETHINK_AUTH_KEY` to be set. +### Using example data -If you don't have access to our database, you can run the build using the +Alternatively, you can run the build using the example data provided in this repository. Before running the build, copy the example sequences into the `data/` directory like so: @@ -61,10 +72,7 @@ With access to AWS, this can be more quickly run as: nextstrain build --aws-batch --aws-batch-cpus 4 --aws-batch-memory 7200 . --jobs 4 [Nextstrain]: https://nextstrain.org -[fauna]: https://github.com/nextstrain/fauna -[augur]: https://github.com/nextstrain/augur -[auspice]: https://github.com/nextstrain/auspice -[snakemake cli]: https://snakemake.readthedocs.io/en/stable/executable.html#all-options -[nextstrain-cli]: https://nextstrain.org/docs/getting-started/container-installation -[nextstrain-snakemake]: https://nextstrain.org/docs/getting-started/local-installation -[quickstart guide]: https://nextstrain.org/docs/getting-started/quickstart +[augur]: https://docs.nextstrain.org/projects/augur/en/stable/ +[auspice]: https://docs.nextstrain.org/projects/auspice/en/stable/index.html +[Installing Nextstrain guide]: https://docs.nextstrain.org/en/latest/install.html +[Running a Pathogen Workflow guide]: https://docs.nextstrain.org/en/latest/tutorials/running-a-workflow.html