Norovirus dengue and COX1 version history - NLM-DIR/vadr GitHub Wiki
Version history of the VADR versions, models and options GenBank has used to
automatically process norovirus, dengue virus and COX1 submissions.
Version history for GenBank submission processing
Dates below are deployment dates (when the build became live for GenBank
submission processing), which are not always the date the build was made.
A row appears whenever the VADR version, the models version, or the
command-line options changed for that virus. Where the options did not change
from the row above, the cell reads no change.
Norovirus
| date |
vadr version |
models version |
command-line options |
notes |
| Jun 22, 2020 |
1.1 |
1.1-1 |
--group Norovirus |
|
| Jul 28, 2020 |
1.1.1 |
1.1-1 |
no change |
|
| Dec 3, 2020 |
1.1.2 |
1.1-1 |
--group Norovirus --nomisc --noprotid |
|
| Feb 19, 2021 |
1.1.3 |
1.1-1 |
no change |
|
| Apr 13, 2021 |
1.2 |
calici-1.2-1 |
no change |
|
| Aug 5, 2021 |
1.3 |
calici-1.2-1 |
--split --cpu 1 --group Norovirus --nomisc --noprotid |
|
| Dec 23, 2021 |
1.4 |
calici-1.2-1 |
no change |
|
| Jan 11, 2022 |
1.4.1 |
calici-1.2-1 |
no change |
|
| Jul 11, 2022 |
1.4.2 |
calici-1.2-1 |
no change |
|
| May 15, 2024 |
1.6.3 |
calici-1.2-1 |
adds -r |
|
| March 12, 2026 |
1.7 |
calici-1.2-1 |
no change |
|
| Sep 3, 2026 |
1.7 |
calici-1.7-2 |
no change |
|
| Oct 8, 2026 |
1.7.3 |
calici-1.7-2 |
no change |
|
Dengue
| date |
vadr version |
models version |
command-line options |
notes |
| Jun 22, 2020 |
1.1 |
1.1-1 |
--group Dengue |
|
| Jul 28, 2020 |
1.1.1 |
1.1-1 |
no change |
|
| Dec 3, 2020 |
1.1.2 |
1.1-1 |
--group Dengue --nomisc --noprotid |
|
| Feb 19, 2021 |
1.1.3 |
1.1-1 |
no change |
|
| Apr 13, 2021 |
1.2 |
flavi-1.2-1 |
adds --mkey flavi |
|
| Aug 5, 2021 |
1.3 |
flavi-1.2-1 |
adds --split --cpu 1 |
|
| Dec 23, 2021 |
1.4 |
flavi-1.2-1 |
no change |
|
| Jan 11, 2022 |
1.4.1 |
flavi-1.2-1 |
no change |
|
| Jul 11, 2022 |
1.4.2 |
flavi-1.2-1 |
no change |
|
| May 15, 2024 |
1.6.3 |
flavi-1.2-1 |
adds -r |
|
| March 12, 2026 |
1.7 |
flavi-1.2-1 |
no change |
|
| Oct 8, 2026 |
1.7.3 |
flavi-1.2-1 |
no change |
|
COX1
| date |
vadr version |
models version |
command-line options |
notes |
| Jun 22, 2020 |
1.1 |
cox1-1.1-1 |
--xmaxdel 3 --xmaxins 3 --xlongest --mkey cox1 --alt_pass lowcovrg --alt_fail fsthicnf,fstlocnf --fstlowthr 0.0 --nomisc |
|
| Jul 28, 2020 |
1.1.1 |
cox1-1.1-1 |
no change |
|
| Dec 3, 2020 |
1.1.2 |
cox1-1.1-4 |
adds --fstminnt 5 --noprotid --xsub $VADRMODELDIR/cox1-1.1-4.phy.xsub |
|
| Feb 19, 2021 |
1.1.3 |
cox1-1.1-4 |
no change |
|
| Apr 13, 2021 |
1.2 |
cox1-1.2-1 |
--xsub path now cox1.phy.xsub |
|
| Aug 5, 2021 |
1.3 |
cox1-1.2-1 |
adds --split --cpu 4; frameshift alerts become fstlocfi,fstlocf5,fstlocf3 with --fstminnti/5/3 5 |
|
| Dec 23, 2021 |
1.4 |
cox1-1.2-1 |
frameshift alerts collapse to fstlocfi,fstlocft with --fstminnti/--fstminntt 5 |
|
| Jan 11, 2022 |
1.4.1 |
cox1-1.2-1 |
no change |
|
| Jul 11, 2022 |
1.4.2 |
cox1-1.2-1 |
no change |
|
| May 15, 2024 |
1.6.3 |
cox1-1.2-2 |
drops --xlongest; adds -r --noflank |
|
| March 12, 2026 |
1.7 |
cox1-1.2-2 |
no change |
|
| Oct 8, 2026 |
1.7.3 |
cox1-1.2-2 |
no change |
|