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Positive Controls #25

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12 of 44 tasks
ktmeaton opened this issue Jun 14, 2022 · 2 comments
Closed
12 of 44 tasks

Positive Controls #25

ktmeaton opened this issue Jun 14, 2022 · 2 comments
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@ktmeaton
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enhancement New feature or request validation
Milestone
v0.5.0

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@ktmeaton
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ktmeaton commented Jun 14, 2022 •
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This is the list of implemented positive controls:

  • XA | Alpha recombinant (poor lineage accuracy)
  • XB | Conflicting designation issue
  • XC | Alpha recombinant (poor lineage accuracy)
  • XD
  • XE
  • XG
  • XH
  • XJ
  • XK | No public genomes
  • XL
  • XM
  • XN
  • XP
  • XQ
  • XR
  • XS
  • XT | No public genomes | Restricted to South Africa
  • XU | No public genomes | Restricted to India, Japan, Australia
  • XW | ...
  • XY | ...
  • XZ | ...
  • XAA | ...
  • XAB | ...
  • XAC | ...
  • XAD | ...
  • XAE | ...
  • XAF | ...
  • XAG | ...
  • XAH | ...
  • XAJ | ...
  • XAK | ...
  • XAL | ...
  • XAM | ...
  • XAN | ...
  • XAP | ...
  • XAQ | ...
  • XAR | ...
  • XAS | ...
  • XAT | ...
  • XAU | ...
  • XAV | ...
  • XAW | ...
  • XAY | ...
  • XAZ | ‼ Priority | Large Lineage
@ktmeaton
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I might file these as separate issues for tracking which controls I've added.

@ktmeaton ktmeaton closed this as completed Aug 4, 2022
@ktmeaton ktmeaton reopened this Sep 8, 2022
@ktmeaton
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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

ktmeaton pushed a commit that referenced this issue Sep 15, 2022
dataset: reduce controls to one sequence per clade for #25,92
a918617
@ktmeaton ktmeaton self-assigned this Sep 16, 2022
@ktmeaton ktmeaton added enhancement New feature or request validation labels Sep 16, 2022
@ktmeaton ktmeaton added this to the v0.4.3 milestone Sep 16, 2022
@ktmeaton ktmeaton mentioned this issue Sep 20, 2022
Closed
ktmeaton pushed a commit that referenced this issue Oct 3, 2022
dataset: reduce controls to one sequence per clade for #25,92
076e14b
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enhancement New feature or request validation
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ncov-recombinant
Status: Done
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v0.5.0
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