v14

From the changelog:

• 23 October 2024: Update workflow to use Nextclade v3. This includes the removal of unused mutation summary script and rules that expected Nextclade v2 outputs. Dropping the mutation summary rules removed the need for the full alignment rule align to produce the insertions and translations outputs, so they have been removed. The build_align rule no longer produces a separate insertions.tsv since insertions are now included in the nextclade_qc.tsv. PR 1160

• 2 October 2024: Include a new parameter for clade_recency under colors. This parameter is used to define which clades should receive a color from the standard rainbow palette. A value of 6M will cause clades with strains in the tree sampled within the last 6 months to be colored and earlier strains to not receive a color (and be colored in a palette of grays by Auspice). This clade_recency parameter is used in builds.yaml in nextstrain_profiles to color clades according for the 1m, 2m, 6m and all-time timepoints. If clade_recency is not supplied then all clades will be colored. PR 1132

• 30 September 2024: Use population-based weighted sampling for nextstrain_profiles. This requires a minimum Augur version of 25.3.0. PRs 1106, 1150, 1151

• 31 January 2024: Remove RBD-level related rules and files since this feature has been broken since May 2023 and is no longer relevant. PR 1097

• 30 January 2024: Fix RBD-level coloring by updating clade label and clade parsing. PR 1094

• 14 Dec 2023: Use nextclade2 binary that makes the version explicit PR 1089

• 17 June 2023: Update subsampling strategy for nextstrain_profiles to better equilibrate per-capita sampling rates across geographic regions. Primarily this update breaks out China and India as separate subsampling targets because of their large population sizes. It also fine tunes the per-region sampling targets. After this update, URL structure (ie https://nextstrain.org/ncov/gisaid/global/6m) is unchanged. PR 1074

v13

From the change log:

• 16 May 2023: Update workflow to support Augur v22 which updates the augur clades interface and structure of the output files to allow specifying the clade label & coloring keys. Because we use custom scripts to parse these files this worflow also needed updating. This change results in a simplifying of the nCoV pipeline (PR 1000).

• 11 April 2023: Elevate XBB.1.16 as new clade 23B. See PR 1059 for the rationale behind this clade update.

• 6 April 2023: Update conda environment dependencies: augur 19.2.0 -> 21.1.0, nextalign/nextclade 2.9.1 -> 2.13.1, iqtree 2.2.0_beta -> 2.2.0.3. PR 1056

• 16 March 2023: Add a build configuration option, nextclade_dataset, to allow users to change the Nextclade dataset used for alignment and quality control. For example, setting nextclade_dataset: sars-cov-2-21L will use the BA.2 (Nextstrain 21L) dataset that provides immune escape and ACE2 binding scores. See the workflow configuration guide for more details. PR 1046

• 30 January 2023: Include new clade 23A correspoding to Pango lineage XBB.1.5. See PR 1043 for the rationale behind this clade update.

• 9 December 2022: Add immune escape and ace2_binding from metadata as colorings for nextstrain-open and nextstrain-gisaid builds. PR 1036

• 24 November 2022: Add "1m" timespan in Nextstrain profile builds. PR 1027

• 24 November 2022: calculate_delta_frequency: Allow script to work with fewer pivots available than requested with --delta-pivots. PR 1027

• 4 November 2022: Deploy individual builds to Nextstrain as soon as they are ready, as opposed to only once all builds are ready to speed up the feedback loop PR #1025

• 3 November 2022: Use weekly grouping for "2m" timespan in Nextstrain profile builds. PR 1023

• 2 November 2022: Make RBD levels filterable PR 1028

• 21 October 2022: Implement RBD-level coloring for BA.2 (21L) descendants. For background on this and lineage definitions please see Variant report 2022-10-17. PR 1018.

v12

From the change log:

• 1 July 2022: Update workflow to support Nextclade v2 (PRs 963, 969). See the Nextclade changelog for more information.

• 1 June 2022: Add "2m" timespan in Nextstrain profile builds. PR 957

• 29 April 2022: Include multiple timespans in Nextstrain profile builds. PR 910

• 29 April 2022: Update default mask parameters to mask 200 bases from the end of the genome rather than the existing 50. This was necessary because there is a large deletion in this region in circulating 21L viruses. This deletion is causing problems with alignment and the resulting mis-alignment appears as excess mutations in the tree. PR 939.

• 27 April 2022: Include new clades 22A, 22B and 22C, where 22A corresponds to Pango lineage BA.4, 22B corresponds to Pango lineage BA.5 and 22C corresponds to Pango lineage BA.2.12.1. Please see PR 933 for rationale behind these clade updates.

• 27 April 2022: Convert to hierarchical clade definitions. This streamlines clade definitions significantly and makes it easier to understand clade relationships. Changes can be seen in defaults/clades.tsv and in PR 855. This feature requires Augur v14.0 or above. To upgrade Augur follow the installation guide at docs.nextstrain.org.

• 12 April 2022: Add support for numbers in build names. PR 524

• 11 April 2022: Update clade definitions to be robust to presence of lineage BA.4 and BA.5 viruses. PR #913

• 17 March 2022: Add Nextclade_pango column to metadata PR 892

• 8 Mar 2022: Support disabling clock filters in the refine step by setting clock_filter_iqd: 0 in the refine section. PR #884, Issue #852.

• 11 February 2022: Add colors to default Auspice config for Nextclade quality control columns and a filter for overall Nextclade QC status. PR #861.

v11

See the change log for more details

v10

Please see the changelog for more details

v9

Please see the changelog for more details

v8

See the change log for more details.

v7

See the change log for more details.

v6

See the change log for more details.

v5

See the change log for more details.