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Update pooling volumes for v4 #75

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merged 4 commits into from
Jan 7, 2022
Merged

Update pooling volumes for v4 #75

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63121a1
Update pooling volumes
Jun 21, 2021
724814c
Update pooling volumes
Jul 6, 2021
8b7860f
Add V4.1 primer scheme
Dec 17, 2021
a937e90
Add insert.bed file
Jan 7, 2022
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37 changes: 37 additions & 0 deletions primer_schemes/nCoV-2019/V4.1/README
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Original file line number Diff line number Diff line change
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This primer scheme is an update to the V4 scheme which restores the funtionality of some primers against the Omicron variant. The following changes are made;

Added to pool 1:
SARS-CoV-2_23_RIGHT_alt1
SARS-CoV-2_27_RIGHT_alt1
SARS-CoV-2_79_RIGHT_alt1
SARS-CoV-2_89_LEFT_alt1
SARS-CoV-2_89_RIGHT_alt1

Added to pool 2:
SARS-CoV-2_10_LEFT_alt1
SARS-CoV-2_10_RIGHT_alt1
SARS-CoV-2_76_LEFT_alt1
SARS-CoV-2_76_RIGHT_alt1
SARS-CoV-2_88_LEFT_alt1
SARS-CoV-2_90_RIGHT_alt1

Guide to pooling volumes are;

2x volume:
SARS-CoV-2_1_LEFT & SARS-CoV-2_1_RIGHT
SARS-CoV-2_7_LEFT & SARS-CoV-2_7_RIGHT
SARS-CoV-2_13_LEFT & SARS-CoV-2_13_RIGHT
SARS-CoV-2_17_LEFT & SARS-CoV-2_17_RIGHT
SARS-CoV-2_27_LEFT & SARS-CoV-2_27_RIGHT
SARS-CoV-2_45_LEFT & SARS-CoV-2_45_RIGHT
SARS-CoV-2_59_LEFT & SARS-CoV-2_59_RIGHT
SARS-CoV-2_60_LEFT & SARS-CoV-2_60_RIGHT
SARS-CoV-2_61_LEFT & SARS-CoV-2_61_RIGHT
SARS-CoV-2_64_LEFT & SARS-CoV-2_64_RIGHT
SARS-CoV-2_79_LEFT & SARS-CoV-2_79_RIGHT
SARS-CoV-2_90_LEFT & SARS-CoV-2_90_RIGHT
SARS-CoV-2_91_LEFT & SARS-CoV-2_91_RIGHT

1x volume:
All other primers including alts.

99 changes: 99 additions & 0 deletions primer_schemes/nCoV-2019/V4.1/SARS-CoV-2.insert.bed
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Original file line number Diff line number Diff line change
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MN908947.3 50 408 SARS-CoV-2_INSERT_1 1 +
MN908947.3 344 705 SARS-CoV-2_INSERT_2 2 +
MN908947.3 666 1017 SARS-CoV-2_INSERT_3 1 +
MN908947.3 966 1337 SARS-CoV-2_INSERT_4 2 +
MN908947.3 1266 1623 SARS-CoV-2_INSERT_5 1 +
MN908947.3 1562 1925 SARS-CoV-2_INSERT_6 2 +
MN908947.3 1875 2228 SARS-CoV-2_INSERT_7 1 +
MN908947.3 2180 2544 SARS-CoV-2_INSERT_8 2 +
MN908947.3 2508 2861 SARS-CoV-2_INSERT_9 1 +
MN908947.3 2850 3156 SARS-CoV-2_INSERT_10 2 +
MN908947.3 3102 3470 SARS-CoV-2_INSERT_11 1 +
MN908947.3 3412 3769 SARS-CoV-2_INSERT_12 2 +
MN908947.3 3705 4067 SARS-CoV-2_INSERT_13 1 +
MN908947.3 4018 4387 SARS-CoV-2_INSERT_14 2 +
MN908947.3 4339 4685 SARS-CoV-2_INSERT_15 1 +
MN908947.3 4648 4995 SARS-CoV-2_INSERT_16 2 +
MN908947.3 4953 5302 SARS-CoV-2_INSERT_17 1 +
MN908947.3 5259 5620 SARS-CoV-2_INSERT_18 2 +
MN908947.3 5584 5932 SARS-CoV-2_INSERT_19 1 +
MN908947.3 5894 6247 SARS-CoV-2_INSERT_20 2 +
MN908947.3 6210 6553 SARS-CoV-2_INSERT_21 1 +
MN908947.3 6507 6859 SARS-CoV-2_INSERT_22 2 +
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MN908947.3 7084 7440 SARS-CoV-2_INSERT_24 2 +
MN908947.3 7403 7747 SARS-CoV-2_INSERT_25 1 +
MN908947.3 7695 8063 SARS-CoV-2_INSERT_26 2 +
MN908947.3 8019 8367 SARS-CoV-2_INSERT_27 1 +
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MN908947.3 19836 20186 SARS-CoV-2_INSERT_66 2 +
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MN908947.3 22428 22785 SARS-CoV-2_INSERT_75 1 +
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MN908947.3 29161 29512 SARS-CoV-2_INSERT_98 2 +
MN908947.3 29475 29827 SARS-CoV-2_INSERT_99 1 +
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