Skip to content

Commit

Permalink
dataset: reduce controls to one sequence per clade for #25,92
Browse files Browse the repository at this point in the history
  • Loading branch information
Katherine Eaton committed Oct 3, 2022
1 parent 77d2210 commit 076e14b
Show file tree
Hide file tree
Showing 10 changed files with 34,466 additions and 45,947 deletions.
8 changes: 1 addition & 7 deletions data/controls-negative/metadata.tsv
View file
Original file line number Diff line number Diff line change
Expand Up @@ -19,18 +19,12 @@ USA/GU-CDC-2-3906074/2021 2021-01-31 USA P.3 21E (Theta) Guam North America MZ77
USA/NY-CDC-LC0031214/2021 2021-03-15 USA B.1.526 21F (Iota) New York North America MW987419.1 Howard et al Z controls-negative
Switzerland/ZH-UZH-IMV-3ba4d945/2021 2021-08-02 Switzerland C.37.1 21G (Lambda) Zürich Europe OU576905.1 ? F controls-negative
USA/FL-CDC-FG-022848/2021 2021-04-12 USA B.1.621 21H (Mu) Florida North America OK213902.1 Howard et al AQ controls-negative
England/MILK-1622A3E/2021 2021-06-03 United Kingdom AY.11 21I (Delta) England Europe OU314327.1 The Lighthouse Lab in Milton et al A controls-negative
USA/FL-CDC-QDX26157271/2021 2021-06-22 USA AY.75 21I (Delta) Florida North America MZ535087.1 Howard et al S controls-negative
USA/TX-CDC-ASC210111920/2021 2021-07-07 USA AY.44 21J (Delta) Texas North America MZ705780.1 Howard et al Q controls-negative
England/QEUH-173F5F0/2021 2021-06-18 United Kingdom AY.4 21J (Delta) England Europe OU358465.1 VanSteenhouse et al A controls-negative
Switzerland/AG-ETHZ-35947998/2022 2022-01-23 Switzerland BA.1.1 21K (Omicron) Aargau Europe OV882645.1 ? G controls-negative
USA/GA-GPHL-2867/2021 2021-12-27 USA BA.1.1.18 21K (Omicron) Georgia North America OM201100.1 Parrott et al controls-negative
Denmark/DCGC-323445/2022 2022-01-15 Denmark BA.2 21L (Omicron) Hovedstaden Europe OW783991.1 Danish Covid-19 Genome et al controls-negative
USA/NY-Broad-CRSP_JYXB4KKAEDIB5CUN/2022 2022-03-07 USA BA.2.7 21L (Omicron) New York North America ON066513.1 Lemieux et al G controls-negative
USA/PA-CDC-QDX34289597/2022 2022-02-25 USA BA.3.1 21M (Omicron) Pennsylvania North America OM998782.1 Howard et al BM controls-negative
USA/NC-CDC-LC0597531/2022 2022-04-22 USA BA.4 22A (Omicron) North Carolina North America ON465569.1 Howard et al CK controls-negative
USA/CA-CDC-LC0603479/2022 2022-04-29 USA BA.4 22A (Omicron) California North America ON468185.1 Howard et al CO controls-negative
USA/FL-BPHL-8585/2022 2022-05-12 USA BA.5 22B (Omicron) Florida North America ON729631.1 Schmedes et al D controls-negative
BHR/22920323375_S6_L001/2022 2022-05-11 Bahrain BA.5 22B (Omicron) Bahrain Asia ON627314.1 Marhoon et al A controls-negative
USA/VT-Broad-CRSP_HCJQO5WTVP7AY6KK/2022 2022-03-28 USA BA.2.12.1 22C (Omicron) Vermont North America ON199482.1 Lemieux et al H controls-negative
USA/RI-CDC-LC0586837/2022 2022-04-13 USA BA.2.12.1 22C (Omicron) Rhode Island North America ON395248.1 Howard et al BZ controls-negative
USA/CA-CDC-LC0797902/2022 2022-07-20 USA BA.2.75 22D (Omicron) California North America OP144984.1 Howard et al BQ controls-negative
8,963 changes: 2,986 additions & 5,977 deletions data/controls-negative/sequences.fasta
View file

Large diffs are not rendered by default.

20 changes: 7 additions & 13 deletions data/controls-positive/metadata.tsv
View file
Original file line number Diff line number Diff line change
@@ -1,29 +1,23 @@
strain date country pango_lineage clade_membership division region genbank_accession author dataset
FRA/IHUMI-6070VR/2022 2022-02-09 France XD Europe OM990739.1 NA controls-positive
FRA/IHUCOVID-64762/2022 2022-02-09 France XD Europe OM990851.1 NA controls-positive
England/MILK-3729AD6/2022 2022-02-16 England XE Europe OW016842.1 NA controls-positive
England/BRBR-3899D04/2022 2022-02-27 England XE Europe OW137497.1 NA controls-positive
England/MILK-36E1AF9/2022 2022-02-14 England XF Europe OW002725.1 NA controls-positive
England/MILK-327F0C5/2022 2022-01-14 England XF Europe OV738853.1 NA controls-positive
England/MILK-3795589/2022 2022-02-19 England XG Europe OW091023.1 NA controls-positive
Scotland/QEUH-37E04A0/2022 2022-02-21 Scotland XG Europe OW084783.1 NA controls-positive
England/MILK-37D141B/2022 2022-02-20 England XH Europe OW042525.1 NA controls-positive
England/MILK-385C31A/2022 2022-02-24 England XH Europe OW126705.1 NA controls-positive
England/MILK-393A26F/2022 2022-03-04 England XJ Europe OW197337.1 NA controls-positive
England/MILK-3BFC759/2022 2022-03-23 England XL Europe OW360896.1 NA controls-positive
England/LSPA-3CC763B/2022 2022-03-28 England XL Europe OW490144.1 NA controls-positive
USA/NY-Broad-CRSP_WH5TJZ42BYV4BC3T/2022 2022-03-28 USA XM North America ON199453.1 NA controls-positive
England/MILK-3796834/2022 2022-02-19 England XM Europe OW090848.1 NA controls-positive
England/LSPA-3B89478/2022 2022-03-20 England XN Europe OW322926.1 NA controls-positive
England/MILK-3B62C6E/2022 2022-03-19 England XN Europe OW320124.1 NA controls-positive
Wales/LSPA-3A9969E/2022 2022-03-13 Wales XR Europe OW286587.1 NA controls-positive
England/LSPA-3B0E8AC/2022 2022-03-15 England XR Europe OW288317.1 NA controls-positive
Scotland/QEUH-38D11C8/2022 2022-03-02 Scotland XP Europe OW159779.1 NA controls-positive
Scotland/QEUH-38CEA2D/2022 2022-03-02 Scotland XP Europe OW156660.1 NA controls-positive
USA/OH-CDC-MMB14658183/2022 2022-03-07 USA XS North America OM981060.1 NA controls-positive
USA/CO-CDC-FG-248528/2022 2022-01-19 USA XS North America OM477123.1 NA controls-positive
England/MILK-38AA91B/2022 2022-02-28 England XQ Europe OW192527.1 NA controls-positive
England/LSPA-3943EF6/2022 2022-03-05 England XQ Europe OW142543.1 NA controls-positive
Switzerland/BE-ETHZ-37580626/2022 2022-05-25 Switzerland XAN Europe OX101390.1 NA controls-positive
Germany/OW765577.1/2022 2022-03-18 Germany XAB Europe OW765577.1 NA controls-positive
USA/TX-CDC-STM-9J566SSEM/2022 2022-06-10 USA XAF North America ON836693.1 NA controls-positive
USA/CA-CDC-QDX37910441/2022 2022-06-09 USA XAN North America ON847076.1 NA controls-positive
Denmark/OX236618.1/2022 2022-07-06 Denmark XAK Europe OX236618.1 NA controls-positive
Denmark/OX214489.1/2022 2022-06-06 Denmark XAL Europe OX214489.1 NA controls-positive
USA/CA-CDC-LC0660066/2022 2022-05-22 USA XAP North America ON660081.1 NA controls-positive
USA/IL-CDC-STM-9T8P4JYCF/2022 2022-07-26 USA XAS North America OP165352.1 NA controls-positive
England/LSPA-3E384C0/2022 2022-05-29 England XAU Europe OX037941.1 NA controls-positive
England/PLYM-3EDDB04/2022 2022-07-11 England XAZ Europe OX241975.1 NA controls-positive
Loading

0 comments on commit 076e14b

Please sign in to comment.