Releases: AKU-CITRIC-Center-for-Bioinformatics/ncov
01222024 - BA Contextuality in Pakistan (BA.x spinoffs)
v2.8.01.22.2024
OS Log:
LSB Version: core-11.1.0ubuntu2-noarch:security-11.1.0ubuntu2-noarch
Distributor ID: Ubuntu
Description: Ubuntu 20.04.5 LTS
Release: 20.04
Codename: focal
Software Log:
nextstrain.cli 7.4.0
augur 22.3.0
IQ-TREE multicore version 1.6.12 for Linux 64-bit built Mar 23 2020
AUSPICE 2.47.0
Genomic Epidemiology of Novel Coronavirus - Pakistan-focused Subsampling (Non-contextual/non-targeted):
Total no. of Pakistan SARS-CoV-2 Genome Sequences downloaded from GISAID (19th January 2024): 4,904
844 strains were dropped during filtering
488 had no metadata
356 of these were dropped because they were in results/Pakistan/excluded_by_diagnostics.txt
1 strains were added back because they were in defaults/include.txt
4,060 strains passed all filters
In this release, only one hCoV-19/Wuhan/WIV04/2019 (WIV04) is used as reference/root (the official reference sequence employed by GISAID; EPI_ISL_402124). WIV04 was chosen because of its high-quality genome sequence and because it represented the consensus of a handful of early submissions for the betacoronavirus responsible for COVID-19 (Pilailuk et al 2020).
Full Change log: (https://github.com/AKU-CITRIC-Center-for-Bioinformatics/ncov/commits/v2.8)
Genomic Epidemiology of Novel Coronavirus - Pakistan and Related Contextual (Targeted) Samples:
Total no. of Global SARS-CoV-2 Genome Sequences downloaded from GISAID (19th January 2024): 4,092
Total no. of Pakistan SARS-CoV-2 Genome Sequences downloaded from GISAID (19th January 2024): 4,904
Total No. of Sequences that passed all filters: 2,599
In this release, only one hCoV-19/Wuhan/WIV04/2019 (WIV04) is used as reference/root (the official reference sequence employed by GISAID; EPI_ISL_402124). WIV04 was chosen because of its high-quality genome sequence and because it represented the consensus of a handful of early submissions for the betacoronavirus responsible for COVID-19 (Pilailuk et al 2020).
Full Change log: (https://github.com/AKU-CITRIC-Center-for-Bioinformatics/ncov/commits/v2.8)
11082023 - BA Contextuality in Pakistan (BA.x spinoffs)
v2.7.11.08.2023
OS Log:
LSB Version: core-11.1.0ubuntu2-noarch:security-11.1.0ubuntu2-noarch
Distributor ID: Ubuntu
Description: Ubuntu 20.04.5 LTS
Release: 20.04
Codename: focal
Software Log:
nextstrain.cli 7.1.0
augur 22.3.0
IQ-TREE multicore version 1.6.12 for Linux 64-bit built Mar 23 2020
AUSPICE 2.47.0
Genomic Epidemiology of Novel Coronavirus - Pakistan-focused Subsampling (Non-contextual/non-targeted):
Total no. of Pakistan SARS-CoV-2 Genome Sequences downloaded from GISAID (7th November 2023): 4,996
Total No. of Sequences Dropped by Nextstrain's Augur Filtering (<27000 nts): 3
359 strains were dropped during filtering
357 of these were dropped because they were in results/Pakistan/excluded_by_diagnostics.txt
2 of these were filtered out by the query: "(root_ref == 'yes' & _length >= 27000) | (pakistan == 'yes' & _length >= 27000)"
1 strains were added back because they were in defaults/include.txt
4,637 strains passed all filters
In this release, only one hCoV-19/Wuhan/WIV04/2019 (WIV04) is used as reference/root (the official reference sequence employed by GISAID; EPI_ISL_402124). WIV04 was chosen because of its high-quality genome sequence and because it represented the consensus of a handful of early submissions for the betacoronavirus responsible for COVID-19 (Pilailuk et al 2020).
Full Change log: (https://github.com/AKU-CITRIC-Center-for-Bioinformatics/ncov/commits/v2.7)
Genomic Epidemiology of Novel Coronavirus - Pakistan and Related Contextual (Targeted) Samples:
Total no. of Global SARS-CoV-2 Genome Sequences downloaded from GISAID (7th November 2023): 3,663
Total no. of Pakistan SARS-CoV-2 Genome Sequences downloaded from GISAID (7th November 2023): 4,996
Total No. of Sequences that passed all filters: 2,746
In this release, only one hCoV-19/Wuhan/WIV04/2019 (WIV04) is used as reference/root (the official reference sequence employed by GISAID; EPI_ISL_402124). WIV04 was chosen because of its high-quality genome sequence and because it represented the consensus of a handful of early submissions for the betacoronavirus responsible for COVID-19 (Pilailuk et al 2020).
Full Change log: (https://github.com/AKU-CITRIC-Center-for-Bioinformatics/ncov/commits/v2.7)
08212023 - BA Contextuality in Pakistan (BA.x spinoffs)
v2.6.08.29.2023
OS Log:
LSB Version: core-11.1.0ubuntu2-noarch:security-11.1.0ubuntu2-noarch
Distributor ID: Ubuntu
Description: Ubuntu 20.04.5 LTS
Release: 20.04
Codename: focal
Software Log:
nextstrain.cli 7.1.0
augur 22.3.0
IQ-TREE multicore version 1.6.12 for Linux 64-bit built Mar 23 2020
AUSPICE 2.47.0
Genomic Epidemiology of Novel Coronavirus - Pakistan-focused Subsampling (Non-contextual/non-targeted):
Total no. of Pakistan SARS-CoV-2 Genome Sequences downloaded from GISAID (18th August 2023): 4,885
Total No. of Sequences Dropped by Nextstrain's Augur Filtering (<27000 nts): 1
355 strains were dropped during filtering
354 of these were dropped because they were in results/Pakistan/excluded_by_diagnostics.txt
1 of these were filtered out by the query: "(root_ref == 'yes' & _length >= 27000) | (pakistan == 'yes' & _length >= 27000)"
1 strains were added back because they were in defaults/include.txt
4,530 strains passed all filters
In this release, only one hCoV-19/Wuhan/WIV04/2019 (WIV04) is used as reference/root (the official reference sequence employed by GISAID; EPI_ISL_402124). WIV04 was chosen because of its high-quality genome sequence and because it represented the consensus of a handful of early submissions for the betacoronavirus responsible for COVID-19 (Pilailuk et al 2020).
Full Change log: (https://github.com/AKU-CITRIC-Center-for-Bioinformatics/ncov/commits/v2.6)
Genomic Epidemiology of Novel Coronavirus - Pakistan and Related Contextual (Targeted) Samples:
Total no. of Global SARS-CoV-2 Genome Sequences downloaded from GISAID (18th August 2023): 3,694
Total no. of Pakistan SARS-CoV-2 Genome Sequences downloaded from GISAID (18th August 2023): 4,885
Total No. of Sequences that passed all filters: 2,741
In this release, only one hCoV-19/Wuhan/WIV04/2019 (WIV04) is used as reference/root (the official reference sequence employed by GISAID; EPI_ISL_402124). WIV04 was chosen because of its high-quality genome sequence and because it represented the consensus of a handful of early submissions for the betacoronavirus responsible for COVID-19 (Pilailuk et al 2020).
Full Change log: (https://github.com/AKU-CITRIC-Center-for-Bioinformatics/ncov/commits/v2.6)
07152023 - BA Contextuality in Pakistan (BA.x spinoffs)
v2.5.07.15.2023
OS Log:
LSB Version: core-11.1.0ubuntu2-noarch:security-11.1.0ubuntu2-noarch
Distributor ID: Ubuntu
Description: Ubuntu 20.04.5 LTS
Release: 20.04
Codename: focal
Software Log:
nextstrain.cli 6.2.1
AUGUR 22.0.1
IQ-TREE multicore version 2.2.2.3 COVID-edition for Linux 64-bit built May 16 2023
AUSPICE 2.46.0
Genomic Epidemiology of Novel Coronavirus - Pakistan-focused Subsampling (Non-contextual/non-targeted):
Total no. of Pakistan SARS-CoV-2 Genome Sequences downloaded from GISAID (14th July 2023): 4,949
Total No. of Sequences Dropped by Nextstrain's Augur Filtering (<27000 nts): 13
562 strains were dropped during filtering
536 of these were dropped because they were in results/Pakistan/excluded_by_diagnostics.txt
13 of these were filtered out by the query: "(root_ref == 'yes' & _length >= 27000) | (pakistan == 'yes' & _length >= 27000)"
13 of these were dropped because of their ambiguous date in any
1 strains were added back because they were in defaults/include.txt
4,387 strains passed all filters
In this release, only one hCoV-19/Wuhan/WIV04/2019 (WIV04) is used as reference/root (the official reference sequence employed by GISAID; EPI_ISL_402124). WIV04 was chosen because of its high-quality genome sequence and because it represented the consensus of a handful of early submissions for the betacoronavirus responsible for COVID-19 (Pilailuk et al 2020).
Full Change log: (https://github.com/AKU-CITRIC-Center-for-Bioinformatics/ncov/commits/v2.5)
Genomic Epidemiology of Novel Coronavirus - Pakistan and Related Contextual (Targeted) Samples:
Total no. of Global SARS-CoV-2 Genome Sequences downloaded from GISAID (14th July 2023): 3,716
Total no. of Pakistan SARS-CoV-2 Genome Sequences downloaded from GISAID (14th July 2023): 4,949
Total No. of Sequences that passed all filters: 2,624
In this release, only one hCoV-19/Wuhan/WIV04/2019 (WIV04) is used as reference/root (the official reference sequence employed by GISAID; EPI_ISL_402124). WIV04 was chosen because of its high-quality genome sequence and because it represented the consensus of a handful of early submissions for the betacoronavirus responsible for COVID-19 (Pilailuk et al 2020).
Full Change log: (https://github.com/AKU-CITRIC-Center-for-Bioinformatics/ncov/commits/v2.5)
05292023 - BA Contextuality in Pakistan (BA.x spinoffs)
v2.4.05.29.2023
OS Log:
LSB Version: core-11.1.0ubuntu2-noarch:security-11.1.0ubuntu2-noarch
Distributor ID: Ubuntu
Description: Ubuntu 20.04.5 LTS
Release: 20.04
Codename: focal
Software Log:
nextstrain.cli 6.2.1
AUGUR 22.0.1
IQ-TREE multicore version 2.2.2.3 COVID-edition for Linux 64-bit built May 16 2023
AUSPICE 2.46.0
Genomic Epidemiology of Novel Coronavirus - Pakistan-focused Subsampling (Non-contextual/non-targeted):
Total no. of Pakistan SARS-CoV-2 Genome Sequences downloaded from GISAID (25th May 2023): 4,790
Total No. of Sequences Dropped by Nextstrain's Augur Filtering (<27000 nts): 13
561 strains were dropped during filtering
539 of these were dropped because they were in results/Pakistan/excluded_by_diagnostics.txt
13 of these were filtered out by the query: "(root_ref == 'yes' & _length >= 27000) | (pakistan == 'yes' & _length >= 27000)"
9 of these were dropped because of their ambiguous date in any
1 strains were added back because they were in defaults/include.txt
4,229 strains passed all filters
In this release, only one hCoV-19/Wuhan/WIV04/2019 (WIV04) is used as reference/root (the official reference sequence employed by GISAID; EPI_ISL_402124). WIV04 was chosen because of its high-quality genome sequence and because it represented the consensus of a handful of early submissions for the betacoronavirus responsible for COVID-19 (Pilailuk et al 2020).
Full Change log: (https://github.com/AKU-CITRIC-Center-for-Bioinformatics/ncov/commits/v2.4)
Genomic Epidemiology of Novel Coronavirus - Pakistan and Related Contextual (Targeted) Samples:
Total no. of Global SARS-CoV-2 Genome Sequences downloaded from GISAID (25 May 2023): 2,722
Total no. of Pakistan SARS-CoV-2 Genome Sequences downloaded from GISAID (25th May 2023): 4,790
Total No. of Sequences that passed all filters: 2,657
In this release, only one hCoV-19/Wuhan/WIV04/2019 (WIV04) is used as reference/root (the official reference sequence employed by GISAID; EPI_ISL_402124). WIV04 was chosen because of its high-quality genome sequence and because it represented the consensus of a handful of early submissions for the betacoronavirus responsible for COVID-19 (Pilailuk et al 2020).
Full Change log: (https://github.com/AKU-CITRIC-Center-for-Bioinformatics/ncov/commits/v2.4)
04172023 - BA Contextuality in Pakistan (BA.x spinoffs)
v2.3.04.17.2023
OS Log:
LSB Version: core-11.1.0ubuntu4-noarch:security-11.1.0ubuntu4-noarch
Distributor ID: Ubuntu
Description: Ubuntu 22.04 LTS
Release: 22.04
Codename: jammy
Software Log:
nextstrain.cli 6.1.0.post1
AUGUR 21.0.1
IQ-TREE multicore version 1.6.12 for Linux 64-bit built Mar 23 2020
AUSPICE 2.44.0
Genomic Epidemiology of Novel Coronavirus - Pakistan-focused Subsampling (Non-contextual/non-targeted):
Total no. of Pakistan SARS-CoV-2 Genome Sequences downloaded from GISAID (14th April 2023): 4,672
Total No. of Sequences Dropped by Nextstrain's Augur Filtering (<27000 nts): 142
531 strains were dropped during filtering
384 of these were dropped because they were in results/Pakistan/excluded_by_diagnostics.txt
142 of these were filtered out by the query: "(root_ref == 'yes' & _length >= 27000) | (pakistan == 'yes' & _length >= 27000)"
9 of these were dropped because of their ambiguous date in any
1 strains were added back because they were in defaults/include.txt
4,137 strains passed all filters
In this release, only one hCoV-19/Wuhan/WIV04/2019 (WIV04) is used as reference/root (the official reference sequence employed by GISAID; EPI_ISL_402124). WIV04 was chosen because of its high-quality genome sequence and because it represented the consensus of a handful of early submissions for the betacoronavirus responsible for COVID-19 (Pilailuk et al 2020).
Full Change log: (https://github.com/AKU-CITRIC-Center-for-Bioinformatics/ncov/commits/v2.3)
Genomic Epidemiology of Novel Coronavirus - Pakistan and Related Contextual (Targeted) Samples:
Total no. of Global SARS-CoV-2 Genome Sequences downloaded from GISAID (14th April 2023): 2,781
Total no. of Pakistan SARS-CoV-2 Genome Sequences downloaded from GISAID (14th April 2023): 4,672
Total No. of Sequences that passed all filters: 2,714
In this release, only one hCoV-19/Wuhan/WIV04/2019 (WIV04) is used as reference/root (the official reference sequence employed by GISAID; EPI_ISL_402124). WIV04 was chosen because of its high-quality genome sequence and because it represented the consensus of a handful of early submissions for the betacoronavirus responsible for COVID-19 (Pilailuk et al 2020).
Full Change log: (https://github.com/AKU-CITRIC-Center-for-Bioinformatics/ncov/commits/v2.3)
03242023 - BA Contextuality in Pakistan (BA.x spinoffs)
v2.2.03.24.2023
OS Log:
LSB Version: core-11.1.0ubuntu4-noarch:security-11.1.0ubuntu4-noarch
Distributor ID: Ubuntu
Description: Ubuntu 22.04 LTS
Release: 22.04
Codename: jammy
Software Log:
Nextstrain.cli v6.1.0.post1
AUGUR v21.0.1
IQ-TREE multicore version v1.6.12 for Linux 64-bit built Mar 23 2020
AUSPICE v2.44.0
Genomic Epidemiology of Novel Coronavirus - Pakistan-focused Subsampling (Non-contextual/non-targeted):
Total no. of Pakistan SARS-CoV-2 Genome Sequences downloaded from GISAID (24th March 2023): 4,572
Total No. of Sequences Dropped by Nextstrain's Augur Filtering (<27000 nts): 142
514 strains were dropped during filtering
367 of these were dropped because they were in results/Pakistan/excluded_by_diagnostics.txt
142 of these were filtered out by the query: "(root_ref == 'yes' & _length >= 27000) | (pakistan == 'yes' & _length >= 27000)"
9 of these were dropped because of their ambiguous date in any
1 strains were added back because they were in defaults/include.txt
4,054 strains passed all filters
In this release, only one hCoV-19/Wuhan/WIV04/2019 (WIV04) is used as reference/root (the official reference sequence employed by GISAID; EPI_ISL_402124). WIV04 was chosen because of its high-quality genome sequence and because it represented the consensus of a handful of early submissions for the betacoronavirus responsible for COVID-19 (Pilailuk et al 2020).
Full Change log: (https://github.com/AKU-CITRIC-Center-for-Bioinformatics/ncov/commits/v2.2)
Genomic Epidemiology of Novel Coronavirus - Pakistan and Related Contextual (Targeted) Samples:
Total no. of Global SARS-CoV-2 Genome Sequences downloaded from GISAID (24th March 2023): 2,823
Total no. of Pakistan SARS-CoV-2 Genome Sequences downloaded from GISAID (24th March 2023): 4,572
Total No. of Sequences that passed all filters: 2,618
In this release, only one hCoV-19/Wuhan/WIV04/2019 (WIV04) is used as reference/root (the official reference sequence employed by GISAID; EPI_ISL_402124). WIV04 was chosen because of its high-quality genome sequence and because it represented the consensus of a handful of early submissions for the betacoronavirus responsible for COVID-19 (Pilailuk et al 2020).
Full Change log: (https://github.com/AKU-CITRIC-Center-for-Bioinformatics/ncov/commits/v2.2)
12192022 - BA Contextuality in Pakistan (BA.x spinoffs)
v2.0.12.19.2022
OS Log:
LSB Version: core-11.1.0ubuntu4-noarch:security-11.1.0ubuntu4-noarch
Distributor ID: Ubuntu
Description: Ubuntu 22.04 LTS
Release: 22.04
Codename: jammy
Software Log:
Nextstrain.cli v4.2.0
AUGUR v17.0.0
IQ-TREE multicore v2.2.0.3 COVID-edition for Linux 64-bit built May 11 2022
AUSPICE v2.29.1
Genomic Epidemiology of Novel Coronavirus - Pakistan-focused Subsampling (Non-contextual/non-targeted):
Total no. of Pakistan SARS-CoV-2 Genome Sequences downloaded from GISAID (17th December 2022): 4,201
Total No. of Sequences Dropped by Nextstrain's Augur Filtering (<27000 nts): 138
446 strains were dropped during filtering
299 of these were dropped because they were in results/Pakistan/excluded_by_diagnostics.txt
138 of these were filtered out by the query: "(root_ref == 'yes' & _length >= 27000) | (pakistan == 'yes' & _length >= 27000)"
9 of these were dropped because of their ambiguous date in any
1 strains were added back because they were in defaults/include.txt
3,755 strains passed all filters
In this release, only one hCoV-19/Wuhan/WIV04/2019 (WIV04) is used as reference/root (the official reference sequence employed by GISAID; EPI_ISL_402124). WIV04 was chosen because of its high-quality genome sequence and because it represented the consensus of a handful of early submissions for the betacoronavirus responsible for COVID-19 (Pilailuk et al 2020).
Full Change log: (https://github.com/AKU-CITRIC-Center-for-Bioinformatics/ncov/commits/v2.0)
Genomic Epidemiology of Novel Coronavirus - Pakistan and Related Contextual (Targeted) Samples:
Total no. of Global SARS-CoV-2 Genome Sequences downloaded from GISAID (17th December 2022): 2,908
Total no. of Pakistan SARS-CoV-2 Genome Sequences downloaded from GISAID (17th December 2022): 4,201
Total No. of Sequences that passed all filters: 2,612
In this release, only one hCoV-19/Wuhan/WIV04/2019 (WIV04) is used as reference/root (the official reference sequence employed by GISAID; EPI_ISL_402124). WIV04 was chosen because of its high-quality genome sequence and because it represented the consensus of a handful of early submissions for the betacoronavirus responsible for COVID-19 (Pilailuk et al 2020).
Full Change log: (https://github.com/AKU-CITRIC-Center-for-Bioinformatics/ncov/commits/v2.0)
11202022 - BA Contextuality in Pakistan (BA.x spinoffs)
v1.9.11.20.2022
OS Log:
LSB Version: core-11.1.0ubuntu4-noarch:security-11.1.0ubuntu4-noarch
Distributor ID: Ubuntu
Description: Ubuntu 22.04 LTS
Release: 22.04
Codename: jammy
Software Log:
Nextstrain.cli v4.2.0
AUGUR v17.0.0
IQ-TREE multicore v2.2.0.3 COVID-edition for Linux 64-bit built May 11 2022
AUSPICE v2.29.1
Genomic Epidemiology of Novel Coronavirus - Pakistan-focused Subsampling (Non-contextual/non-targeted):
Total no. of Pakistan SARS-CoV-2 Genome Sequences downloaded from GISAID (18th November 2022): 4,147
Total No. of Sequences Dropped by Nextstrain's Augur Filtering (<27000 nts): 134
440 strains were dropped during filtering
297 of these were dropped because they were in results/Pakistan/excluded_by_diagnostics.txt
134 of these were filtered out by the query: "(root_ref == 'yes' & _length >= 27000) | (pakistan == 'yes' & _length >= 27,000)"
9 of these were dropped because of their ambiguous date in any
1 strains were added back because they were in defaults/include.txt
3,707 strains passed all filters
In this release, only one hCoV-19/Wuhan/WIV04/2019 (WIV04) is used as reference/root (the official reference sequence employed by GISAID; EPI_ISL_402124). WIV04 was chosen because of its high-quality genome sequence and because it represented the consensus of a handful of early submissions for the betacoronavirus responsible for COVID-19 (Pilailuk et al 2020).
Full Change log: (https://github.com/AKU-CITRIC-Center-for-Bioinformatics/ncov/commits/v1.9)
Genomic Epidemiology of Novel Coronavirus - Pakistan and Related Contextual (Targeted) Samples:
Total no. of Global SARS-CoV-2 Genome Sequences downloaded from GISAID (18th November 2022): 2,943
Total no. of Pakistan SARS-CoV-2 Genome Sequences downloaded from GISAID (18th November 2022): 4,147
Total No. of Sequences that passed all filters: 2,630
In this release, only one hCoV-19/Wuhan/WIV04/2019 (WIV04) is used as reference/root (the official reference sequence employed by GISAID; EPI_ISL_402124). WIV04 was chosen because of its high-quality genome sequence and because it represented the consensus of a handful of early submissions for the betacoronavirus responsible for COVID-19 (Pilailuk et al 2020).
Full Change log: (https://github.com/AKU-CITRIC-Center-for-Bioinformatics/ncov/commits/v1.9)
10212022 - BA Contextuality in Pakistan (BA.x spinoffs)
v1.8.10.21.2022
OS Log:
LSB Version: core-11.1.0ubuntu4-noarch:security-11.1.0ubuntu4-noarch
Distributor ID: Ubuntu
Description: Ubuntu 22.04 LTS
Release: 22.04
Codename: jammy
Software Log:
Nextstrain.cli v4.2.0
AUGUR v17.0.0
IQ-TREE multicore v2.2.0.3 COVID-edition for Linux 64-bit built May 11 2022
AUSPICE v2.29.1
Genomic Epidemiology of Novel Coronavirus - Pakistan-focused Subsampling (Non-contextual/non-targeted):
Total no. of Pakistan SARS-CoV-2 Genome Sequences downloaded from GISAID (20th October 2022): 4,053 (low coverage excluded)
Total No. of Sequences Dropped by Nextstrain's Augur Filtering (<27000 nts): 438
438 strains were dropped during filtering
295 of these were dropped because they were in results/Pakistan/excluded_by_diagnostics.txt
134 of these were filtered out by the query: "(root_ref == 'yes' & _length >= 27000) | (pakistan == 'yes' & _length >= 27000)"
9 of these were dropped because of their ambiguous date in any
1 strains were added back because they were in defaults/include.txt
3,615 strains passed all filters
In this release, only one hCoV-19/Wuhan/WIV04/2019 (WIV04) is used as reference/root (the official reference sequence employed by GISAID; EPI_ISL_402124). WIV04 was chosen because of its high-quality genome sequence and because it represented the consensus of a handful of early submissions for the betacoronavirus responsible for COVID-19 (Pilailuk et al 2020).
Full Change log: (https://github.com/AKU-CITRIC-Center-for-Bioinformatics/ncov/commits/v1.8)
Genomic Epidemiology of Novel Coronavirus - Pakistan and Related Contextual (Targeted) Samples:
Total no. of Global SARS-CoV-2 Genome Sequences downloaded from GISAID (20th October 2022): 3,001
Total no. of Pakistan SARS-CoV-2 Genome Sequences downloaded from GISAID (20th October 2022): 4,053 (low coverage excluded)
Total No. of Sequences that passed all filters: 2,618
In this release, only one hCoV-19/Wuhan/WIV04/2019 (WIV04) is used as reference/root (the official reference sequence employed by GISAID; EPI_ISL_402124). WIV04 was chosen because of its high-quality genome sequence and because it represented the consensus of a handful of early submissions for the betacoronavirus responsible for COVID-19 (Pilailuk et al 2020).
Full Change log: (https://github.com/AKU-CITRIC-Center-for-Bioinformatics/ncov/commits/v1.8)