Comments (2)
I might file these as separate issues for tracking which controls I've added.
from ncov-recombinant.
Simplifying the positive controls to one sample per lineage:
strain | date | country | pango_lineage | region | genbank_accession |
---|---|---|---|---|---|
FRA/IHUCOVID-64762/2022 | 2022-02-09 | France | XD | Europe | OM990851.1 |
England/MILK-3729AD6/2022 | 2022-02-16 | England | XE | Europe | OW016842.1 |
England/MILK-327F0C5/2022 | 2022-01-14 | England | XF | Europe | OV738853.1 |
Scotland/QEUH-37E04A0/2022 | 2022-02-21 | Scotland | XG | Europe | OW084783.1 |
England/MILK-37D141B/2022 | 2022-02-20 | England | XH | Europe | OW042525.1 |
England/MILK-393A26F/2022 | 2022-03-04 | England | XJ | Europe | OW197337.1 |
England/MILK-3BFC759/2022 | 2022-03-23 | England | XL | Europe | OW360896.1 |
USA/NY-Broad-CRSP_WH5TJZ42BYV4BC3T/2022 | 2022-03-28 | USA | XM | North America | ON199453.1 |
England/MILK-3B62C6E/2022 | 2022-03-19 | England | XN | Europe | OW320124.1 |
Wales/LSPA-3A9969E/2022 | 2022-03-13 | Wales | XR | Europe | OW286587.1 |
Scotland/QEUH-38D11C8/2022 | 2022-03-02 | Scotland | XP | Europe | OW159779.1 |
USA/CO-CDC-FG-248528/2022 | 2022-01-19 | USA | XS | North America | OM477123.1 |
England/MILK-38AA91B/2022 | 2022-02-28 | England | XQ | Europe | OW192527.1 |
Germany/OW765577.1/2022 | 2022-03-18 | Germany | XAB | Europe | OW765577.1 |
USA/TX-CDC-STM-9J566SSEM/2022 | 2022-06-10 | USA | XAF | North America | ON836693.1 |
USA/CA-CDC-QDX37910441/2022 | 2022-06-09 | USA | XAN | North America | ON847076.1 |
Denmark/OX236618.1/2022 | 2022-07-06 | Denmark | XAK | Europe | OX236618.1 |
Denmark/OX214489.1/2022 | 2022-06-06 | Denmark | XAL | Europe | OX214489.1 |
USA/CA-CDC-LC0660066/2022 | 2022-05-22 | USA | XAP | North America | ON660081.1 |
USA/IL-CDC-STM-9T8P4JYCF/2022 | 2022-07-26 | USA | XAS | North America | OP165352.1 |
England/LSPA-3E384C0/2022 | 2022-05-29 | England | XAU | Europe | OX037941.1 |
England/PLYM-3EDDB04/2022 | 2022-07-11 | England | XAZ | Europe | OX241975.1 |
from ncov-recombinant.
Related Issues (20)
- Provider more parameters to plot and plot_historical to reduce clutter
- Add GISAID accessKey option for sc2rf
- CI: setup-miniconda failure
- UserWarning: Tight layout not applied. The bottom and top margins cannot be made large enough to accommodate all axes decorations. HOT 1
- validate doesn't check status
- VOC 2023
- Immune Escape Ranking HOT 1
- VirusSeq Canada HOT 2
- Auto-pass sc2rf negatives are missing when exclude_negatives is set to true HOT 2
- Add citation CFF
- AttributeError: 'NoneType' object has no attribute 'startswith'
- proposed1658 | BQ.1.8, XBF(?) or CJ.1(?) HOT 1
- Add XBF to sc2rf voc-2023 now that is a VUM according to WHO
- Investigate the incorporation of OpenRDP
- Make metadata 100% optional.
- Recombinant aliases (EK = XBB.1.5.13)
- Nextclade dataset download error
- Investigate use of freyja barcodes
- IndexError: list index out of range
- Use pango-sequences data as controls
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from ncov-recombinant.