From 4ff6427031d32e6f6ea3bea90c26a43c2f4ff044 Mon Sep 17 00:00:00 2001 From: John SJ Anderson Date: Wed, 28 Aug 2024 10:33:50 -0700 Subject: [PATCH] Augur v25 blog post [#1003] --- .../blog/2024-09-03-augur-v25-features.md | 123 ++++++++++++++++++ 1 file changed, 123 insertions(+) create mode 100644 static-site/content/blog/2024-09-03-augur-v25-features.md diff --git a/static-site/content/blog/2024-09-03-augur-v25-features.md b/static-site/content/blog/2024-09-03-augur-v25-features.md new file mode 100644 index 000000000..0970e6be8 --- /dev/null +++ b/static-site/content/blog/2024-09-03-augur-v25-features.md @@ -0,0 +1,123 @@ +--- +author: "The Nextstrain team" +date: "2024-09-03" +title: "Notable changes in Augur v25" +--- + +The Nextstrain team has released several new versions of Augur – our +bioinformatics toolkit that assists with phylogenomic analyses – over +the past few months. We wanted to highlight some of the significant +feature improvements in these new releases. + +### Excel and OpenOffice support + +One of the features we are most excited to announce is that the +[`augur curate`][] command now supports both Excel (`.xlsx` and +`.xls`) and OpenOffice (`.ods`) files as metadata inputs. This allows +the easy conversion of Excel or OpenOffice files into the expected +metadata TSV used by other Augur commands. *This new feature is +available in Augur v25.2 and later.* + +### Merging multiple metadata files + +We are also very pleased to announce a new command, [`augur merge`][], +which allows for generalized merging of two or more metadata tables +based on a common field. We hope that this will make curation of +metadata inputs significantly easier. We also expect that this will +facilitate starting with existing pathogen repos with curated data +available via [data.nextstrain.org][] and “spiking in” extra, +non-public metadata for additional analysis. We plan to extend this +functionality to support merging of sequence files in a future Augur +release. *The merge feature is available in Augur v25.3 and later.* + +### Weighted sampling + +We have extended `augur filter` with a new flag, +[`--group-by-weights`][], that adds weighted sampling. This allows +subsampling to follow quantities like population size or case counts +to facilitate more representative analyses. Or conversely, this allows +for sampling of a specific “focal” region with more intensity than +other “contextual” regions. This is described in detail in an updated +[Filtering and Subsampling guide][], as well as the help text of the +`--group-by-weights` flag. *This new flag is available in Augur +v25.3 and later.* + +### Generalized read/write commands + +We have added two new I/O related commands, [`augur read-file`][] and +[`augur write-file`][]. By piping to/from these new commands, external +programs can do I/O “the Augur way”, including transparent handling of +compression formats and newlines consistent with the rest of Augur. We +hope that exposing this functionality will make it easier to integrate +external programs into Augur pipelines in a consistent, convenient +way. *These new commands are available in Augur v25.3 and later.* + +### Six new augur curate commands for transforming metadata + +We added a number of new sub commands to [`augur curate`][]. These +commands ease the manipulation of various sorts of dataset metadata: + +* [`augur curate abbreviate-authors`][] abbreviates author lists to + "<first author>, et al." +* [`augur curate apply-geolocation-rules`][] applies user-curated + geolocation rules to geolocation fields +* [`augur curate apply-record-annotations`][] applies user-curated + annotations to existing fields +* [`augur curate parse-genbank-location`][] parses the `geo_loc_name` + field from GenBank records +* [`augur curate rename`][] renames field / column names. +* [`augur curate transform-strain-name`][] filters strain names using + a regular expression + +*All of these new sub-commands are available in Augur v25.0 and later.* + +### Reduction in Auspice JSON sizes of around 30% + +[`augur export v2`][] now limits numerical precision on floats in the +exported JSON file. This should not change how a dataset is displayed +or interpreted in Auspice, but reduces the gzipped and minimised JSON +file size by around 30%, depending on the dataset. This will improve +page load times in Auspice and nextstrain.org. *This change is present +in Augur v25.2 and later.* + +### Debug mode (verbose logging) + +We added a new debugging mode to the entire Augur suite, which is +enabled by setting the `AUGUR_DEBUG` environment variable to a +non-empty value (e.g., `export AUGUR_DEBUG=1`). + +Currently, setting this variable only causes Augur commands to print +additional information about the specifics of handled (i.e., +anticipated) errors. For example, stack traces and parent exceptions +in an exception chain, which are normally not displayed, will be +included when this variable is set. + +In future Augur releases, we anticipate using this variable to +conditionalize new debugging and troubleshooting features, such as +verbose operation logging. *This debugging mode is available in Augur +v25.3 and later.* + +### Thanks + +Thanks for reading our summary of new Augur features! We hope they +prove to be useful in your Augur pipelines and workflows. We welcome +feedback about these new features, and suggestions for additional +ones, either via our [discussion site][], or by opening issues in the +[Augur GitHub][] repo. + +[`augur curate`]: https://docs.nextstrain.org/projects/augur/en/stable/usage/cli/curate/index.html +[`augur merge`]: https://docs.nextstrain.org/projects/augur/en/latest/usage/cli/merge.html +[data.nextstrain.org]: https://data.nextstrain.org +[`--group-by-weights`]: https://docs.nextstrain.org/projects/augur/en/stable/usage/cli/filter.html#augur-make_parser-subsampling +[Filtering and Subsampling guide]: https://docs.nextstrain.org/en/latest/guides/bioinformatics/filtering-and-subsampling.html +[`augur read-file`]: https://docs.nextstrain.org/projects/augur/en/stable/usage/cli/read-file.html +[`augur write-file`]: https://docs.nextstrain.org/projects/augur/en/stable/usage/cli/write-file.html +[`augur curate abbreviate-authors`]: https://docs.nextstrain.org/projects/augur/en/stable/usage/cli/curate/abbreviate-authors.html +[`augur curate apply-geolocation-rules`]: https://docs.nextstrain.org/projects/augur/en/stable/usage/cli/curate/apply-geolocation-rules.html +[`augur curate apply-record-annotations`]: https://docs.nextstrain.org/projects/augur/en/stable/usage/cli/curate/apply-record-annotations.html +[`augur curate parse-genbank-location`]: https://docs.nextstrain.org/projects/augur/en/stable/usage/cli/curate/parse-genbank-location.html +[`augur curate rename`]: https://docs.nextstrain.org/projects/augur/en/stable/usage/cli/curate/rename.html +[`augur curate transform-strain-name`]: https://docs.nextstrain.org/projects/augur/en/stable/usage/cli/curate/transform-strain-name.html +[`augur export v2`]: https://docs.nextstrain.org/projects/augur/en/stable/usage/cli/export.html#v2 +[discussion site]: https://discussion.nextstrain.org/ +[Augur GitHub]: https://github.com/nextstrain/augur