ncov-recombinant
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ktmeaton
Reproducible workflow for SARS-CoV-2 recombinant sequence detection.
Fasta: https://github.com/corneliusroemer/pango-sequences/blob/main/data/pango-consensus-sequences_genome-nuc.fasta.zst
Error in rule `sc2rf_recombinants` ```python File "ncov-recombinant/sc2rf/postprocess.py", line 1334 in main l_node = [c for c in tree.find_clades(l)][0] IndexError: list index out of range ``` I think the solution is...
Barcodes file: https://github.com/andersen-lab/Freyja/blob/main/freyja/data/usher_barcodes.csv
```text Error in rule nextclade_dataset: ... 1: error sending request for url (https://data.master.clades.nextstrain.org/datasets/sars-cov-2/references/MN908947/versions/2023-02-01T12:00:00Z/files/reference.fasta): error trying to connect: Connection reset by peer (os error 104) 2: error trying to connect: Connection...
At this point, only the "strain" column is required, which can be pulled from the fasta sequences.
There are now recombinant aliases (ex. EK = XBB.1.5.13). Remove any code logic that assumes "starts with X". - [ ] Update `postprocess.py`
- pango-designation issue: [#1658](https://github.com/cov-lineages/pango-designation/issues/1658) - covSPECTRUM query: TBD ## Parents **Clade**: `BA.5.3`,`CJ.1` **Lineage**: `BQ.1.8*`,`BA.2*` **Lineage Confidence**: `0.993`,`0.977` ## Immunity **RBD Level**: `6` **RBD Substitutions**: `S:K444T`,`S:L452R`,`S:N460K`,`S:F486P`,`S:F490S`,`S:R493Q` **Immune Escape**: `0.7621` **ACE2 Binding**:...
`v0.7.0` (2023-02-23) |lineage|rbd_level|immune_escape|ace2_binding| |:------|:--------|:------------|:-----------| |XBL |7 |0.9070 |1.0124 | |XBB.1.5|7 |0.9070 |1.0124 | |XBB |7 |0.9070 |0.4069 | |XBN |7 |0.9070 |0.4069 | |XBB.1 |7 |0.9070 |0.4069 | |XBK |6...
https://github.blog/changelog/2022-09-22-github-actions-all-actions-will-begin-running-on-node16-instead-of-node12/