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Merge pull request #193 from nextstrain/sc2-bandwidth
Increase excessBandwidth for SC2 datasets
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data_output/nextstrain/sars-cov-2/BA.2.86/unreleased/CHANGELOG.md
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| ## Unreleased | ||
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| - fix: Increase Nextclade alignment parameter "excessBandwidth" from 9 to 12 to correctly align complex series of indels that has arisen in Spike NTD with the occurrence of S:31- in some JN.1. The bandwidth is chosen to be as small as possible (to ensure fast runtime) but as large as necessary for correct alignment. As a result, occasional adjustments like here are required. Nothing else is changed in this SARS-CoV-2 dataset update. | ||
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| ## 2024-04-15T15:08:22Z | ||
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| - Nextstrain clades 24A (JN.1) and 24B (JN.1.11.1) are now included. | ||
| - All 83 Pango lineages designated between 2024-02-13 and 2024-04-12 are now included, unfold below to see a list of all newly included lineages with their designation dates: | ||
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| <details> | ||
| <summary> Newly included lineages, with designation date in parentheses</summary> | ||
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| - JN.1.23 (2024-02-20) | ||
| - KP.1 (2024-02-22) | ||
| - JN.1.7.1 (2024-03-01) | ||
| - JN.1.7.2 (2024-03-01) | ||
| - KQ.1 (2024-03-01) | ||
| - JN.1.13.1 (2024-03-01) | ||
| - JN.1.1.5 (2024-03-01) | ||
| - KR.1 (2024-03-04) | ||
| - KP.1.1 (2024-03-04) | ||
| - KP.2 (2024-03-04) | ||
| - JN.1.24 (2024-03-04) | ||
| - XDK.1 (2024-03-04) | ||
| - JN.1.25 (2024-03-04) | ||
| - JN.1.25.1 (2024-03-04) | ||
| - XDQ.1 (2024-03-04) | ||
| - JQ.2 (2024-03-05) | ||
| - JN.13 (2024-03-06) | ||
| - JN.13.1 (2024-03-06) | ||
| - JN.1.1.6 (2024-03-09) | ||
| - JN.1.26 (2024-03-09) | ||
| - JN.1.27 (2024-03-09) | ||
| - JN.1.4.4 (2024-03-09) | ||
| - JN.1.8.2 (2024-03-09) | ||
| - JN.1.28 (2024-03-09) | ||
| - JN.1.1.7 (2024-03-09) | ||
| - JN.1.29 (2024-03-09) | ||
| - JN.1.4.5 (2024-03-14) | ||
| - JN.1.18.1 (2024-03-14) | ||
| - JN.1.30 (2024-03-14) | ||
| - JN.1.31 (2024-03-14) | ||
| - JN.1.16.1 (2024-03-14) | ||
| - KS.1 (2024-03-14) | ||
| - JN.1.4.6 (2024-03-14) | ||
| - JN.1.32 (2024-03-14) | ||
| - GE.1.2.2 (2024-03-17) | ||
| - KT.1 (2024-03-17) | ||
| - KT.1.1 (2024-03-17) | ||
| - KT.1.2 (2024-03-17) | ||
| - KP.3 (2024-03-17) | ||
| - JN.1.33 (2024-03-17) | ||
| - JN.1.34 (2024-03-17) | ||
| - JN.1.35 (2024-03-17) | ||
| - JN.1.36 (2024-03-17) | ||
| - KP.2.1 (2024-03-19) | ||
| - KP.2.2 (2024-03-19) | ||
| - JN.1.30.1 (2024-03-19) | ||
| - JQ.2.1 (2024-03-20) | ||
| - XDD.1.1.1 (2024-03-25) | ||
| - KU.1 (2024-03-25) | ||
| - KU.2 (2024-03-25) | ||
| - JN.1.18.2 (2024-03-25) | ||
| - JN.1.36.1 (2024-03-25) | ||
| - KV.1 (2024-03-25) | ||
| - JN.1.37 (2024-03-25) | ||
| - JN.1.28.1 (2024-03-25) | ||
| - KW.1 (2024-03-25) | ||
| - JN.1.38 (2024-03-25) | ||
| - JN.1.39 (2024-03-25) | ||
| - JN.1.40 (2024-03-25) | ||
| - JN.1.41 (2024-03-25) | ||
| - JN.1.42 (2024-03-25) | ||
| - JN.1.43 (2024-03-25) | ||
| - JN.1.43.1 (2024-03-25) | ||
| - KP.1.1.1 (2024-03-25) | ||
| - JN.1.44 (2024-03-25) | ||
| - XDU (2024-03-26) | ||
| - XDP.1 (2024-03-26) | ||
| - JN.2.2.1 (2024-03-26) | ||
| - JN.1.8.3 (2024-03-29) | ||
| - KY.1 (2024-03-29) | ||
| - JN.14 (2024-03-29) | ||
| - JN.1.45 (2024-03-29) | ||
| - XDV (2024-04-02) | ||
| - XDV.1 (2024-04-02) | ||
| - JN.1.42.1 (2024-04-02) | ||
| - JN.1.46 (2024-04-02) | ||
| - JN.1.4.7 (2024-04-02) | ||
| - KV.2 (2024-04-02) | ||
| - KW.1.1 (2024-04-03) | ||
| - KZ.1 (2024-04-04) | ||
| - KZ.1.1 (2024-04-04) | ||
| - KZ.1.1.1 (2024-04-04) | ||
| - JN.1.7.3 (2024-04-04) | ||
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| </details> | ||
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| ## 2024-02-16T04:00:32Z | ||
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| - All 35 Pango lineages designated between 2024-01-16 and 2024-02-12 are now included, unfold below to see a list of all newly included lineages with their designation dates: | ||
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| <details> | ||
| <summary> Newly included lineages, with designation date in parentheses</summary> | ||
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| - XDN (2024-01-16) | ||
| - XDP (2024-01-16) | ||
| - JN.3.2 (2024-01-16) | ||
| - JN.3.2.1 (2024-01-16) | ||
| - JN.11 (2024-01-21) | ||
| - JN.1.12 (2024-01-21) | ||
| - JN.12 (2024-01-22) | ||
| - JN.1.11.1 (2024-01-22) | ||
| - KM.1 (2024-01-31) | ||
| - BA.2.87 (2024-02-01) | ||
| - BA.2.87.1 (2024-02-01) | ||
| - XDQ (2024-02-01) | ||
| - GK.1.10.1 (2024-02-01) | ||
| - XDR (2024-02-01) | ||
| - JN.1.13 (2024-02-01) | ||
| - JN.1.14 (2024-02-01) | ||
| - JN.1.15 (2024-02-01) | ||
| - JN.1.4.1 (2024-02-01) | ||
| - JN.1.2.1 (2024-02-01) | ||
| - JN.1.16 (2024-02-01) | ||
| - JN.1.17 (2024-02-01) | ||
| - JN.1.4.2 (2024-02-02) | ||
| - JN.1.18 (2024-02-04) | ||
| - JN.1.19 (2024-02-04) | ||
| - JN.1.20 (2024-02-04) | ||
| - XDS (2024-02-04) | ||
| - JN.1.9.1 (2024-02-04) | ||
| - JN.1.21 (2024-02-04) | ||
| - JN.1.22 (2024-02-04) | ||
| - JN.1.4.3 (2024-02-12) | ||
| - XDT (2024-02-12) | ||
| - HK.13.2.1 (2024-02-12) | ||
| - KN.1 (2024-02-12) | ||
| - KN.1.1 (2024-02-12) | ||
| - JN.1.1.4 (2024-02-12) | ||
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| </details> | ||
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| ## 2024-01-16T20:31:02Z | ||
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| Initial release of this v3 dataset. | ||
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| This dataset is new to v3 and does not have a v2 equivalent. |
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data_output/nextstrain/sars-cov-2/BA.2.86/unreleased/README.md
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| # SARS-CoV-2 dataset with mutations relative to BA.2.86 | ||
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| | Key | Value | | ||
| | ----------------- | ---------------------------------------------------------------------------------------------------------------------------------------------------------------- | | ||
| | authors | [Cornelius Roemer](https://neherlab.org), [Richard Neher](https://neherlab.org), [Nextstrain](https://nextstrain.org) | | ||
| | reference | `Wuhan-Hu-1/2019` with BA.2.86 SNPs added | | ||
| | workflow | https://github.com/neherlab/nextclade_data_workflows/tree/v3-sc2/sars-cov-2 | | ||
| | path | `nextstrain/sars-cov-2/BA.2.86` | | ||
| | clade definitions | [Nextstrain clades](https://nextstrain.org/blog/2022-04-29-SARS-CoV-2-clade-naming-2022) and [Pango lineages](https://www.nature.com/articles/s41564-020-0770-5) | | ||
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| ## Scope of this dataset | ||
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| This dataset shows mutations relative to the prototypical BA.2.86 sequence and is particularly useful for the analysis of SARS-CoV-2 sequences that are descended from BA.2.86. | ||
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| For the analysis of non-BA.2.86 sequences, other Nextclade datasets for SARS-CoV-2 may be more appropriate. In addition, the `wuhan-hu-1/proteins` dataset shows amino acid mutations in coordinates of mature proteins (nsp1-16) instead of ORF1a and ORF1b coordinates. | ||
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| ## Reference sequence and reference tree | ||
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| The reference sequence in this dataset is `Wuhan-Hu-1/2019` but with BA.2.86 SNPs added. SNPs (but not indels) are thus shown with respect to BA.2.86 while the mutation positions remain within the familiar `Wuhan-Hu-1` coordinate system. | ||
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| The reference tree contains one sequence for each Pango lineage descended from BA.2 (including recombinants such as XBB) and is rooted on BA.2. | ||
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| ## Features | ||
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| This dataset supports: | ||
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| - Assignment of Nextstrain clades | ||
| - Assignment of Pango lineages | ||
| - Sequence QC | ||
| - Phylogenetic placement | ||
| - Calculation of ACE2 binding scores relative to BA.2.86 as described in [Starr et al. 2022](https://doi.org/10.1371/journal.ppat.1010951) | ||
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| ## Nextstrain clades | ||
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| Since its emergence in late 2019, SARS-CoV-2 has evolved into many co-circulating variants. To facilitate discussion of these variants, we have grouped them into clades which are defined by specific signature mutations. | ||
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| Nextstrain clade names consist of two numbers representing a year and then a single letter representing the clade within that year. For example, 21A is the first clade we named in 2021. | ||
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| We define each clade by a combination of signature mutations. You can find the exact clade definition on Github in this [file](https://github.com/nextstrain/ncov/blob/master/defaults/clades.tsv). | ||
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| Below is an illustration of the phylogenetic relationships of Nextstrain clades ([source](https://github.com/nextstrain/ncov-clades-schema/)): | ||
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|  | ||
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| Learn more about how Nextclade assigns clades in the [documentation](https://docs.nextstrain.org/projects/nextclade/en/stable/user/algorithm/). | ||
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| ## What are Nextclade datasets | ||
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| Read more about Nextclade datasets in the Nextclade documentation: https://docs.nextstrain.org/projects/nextclade/en/stable/user/datasets.html |
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