Releases: AKU-CITRIC-Center-for-Bioinformatics/ncov
01262022 - Omicron Contextuality in Pakistan
v0.7.01.26.2022
OS Log:
LSB Version: core-11.1.0ubuntu2-noarch:security-11.1.0ubuntu2-noarch
Distributor ID: Ubuntu
Description: Ubuntu 20.04.3 LTS
Release: 20.04
Codename: focal
Software Log:
Nextstrain.cli v3.0.4
AUGUR v13.1.0
IQ-TREE multicore v2.1.4-beta COVID-edition for Linux 64-bit built Jun 24 2021
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 (24th January 2022): 1,749
Total No. of Sequences Dropped by Nextstrain's Augur Filtering (<27000 nts): 288
14 had no sequence data
335 strains were dropped during filtering
2 of these were dropped because they were in defaults/exclude.txt
33 of these were dropped because of their ambiguous date in any
288 of these were dropped because they were shorter than minimum length of 27000bp
1,414 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/v0.7)
Genomic Epidemiology of Novel Coronavirus - Pakistan and Related Contextual (Targeted) Samples:
Total no. of Global SARS-CoV-2 Genome Sequences downloaded from GISAID (24th January 2022): 3,333
Total no. of Pakistan SARS-CoV-2 Genome Sequences downloaded from GISAID (24th January 2022): 1,749
Total No. of Sequences that passed all filters: 2,365
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/v0.7)
01052022 - Omicron Contextuality in Pakistan
v0.6.01.05.2022
Genomic Epidemiology of Novel Coronavirus - Pakistan-focused Subsampling (Non-contextual/non-targeted):
Total no. of Pakistan SARS-CoV-2 Genome Sequences downloaded from GISAID (05th January 2022): 1,701
Total No. of Sequences Dropped by Nextstrain's Augur Filtering (<27000 nts): 267
18 had no sequence data
6 of these were dropped because they were in defaults/exclude.txt
34 of these were dropped because of their ambiguous date in any
267 of these were dropped because they were shorter than minimum length of 27,000bp
284 strains were dropped during filtering
1,383 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/v0.6
Genomic Epidemiology of Novel Coronavirus - Pakistan and Related Contextual (Targeted) Samples:
Total No. of Global SARS-CoV-2 Genome Sequences downloaded from GISAID (05th January 2022): 3,507
Total No. of Pakistan SARS-CoV-2 Genome Sequences downloaded from GISAID (05th January 2022): 1,701
Total No. of Sequences that passed all filters: 2,353
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/v0.6
12172021 - Omicron Contextuality in Pakistan
v0.5.12.17.2021
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 December 2021): 1,598
Total No. of Sequences Dropped by Nextstrain's Augur Filtering (<27000 nts): 239
12 had no sequence data
2 of these were dropped because they were in defaults/exclude.txt
34 of these were dropped because of their ambiguous date in any
239 of these were dropped because they were shorter than minimum length of 27,000bp
284 strains were dropped during filtering
1,306 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/v0.5
Genomic Epidemiology of Novel Coronavirus - Pakistan and Related Contextual (Targeted) Samples:
Total No. of Global SARS-CoV-2 Genome Sequences downloaded from GISAID (14th December 2021): 3,598
Total No. of Pakistan SARS-CoV-2 Genome Sequences downloaded from GISAID (14th December 2021): 1,598
Total No. of Sequences that passed all filters: 2,285
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/v0.5
12072021
v0.4.12.07.2021
Genomic Epidemiology of Novel Coronavirus - Pakistan-focused Subsampling (Non-contextual/non-targeted):
Total No. of Pakistan SARS-CoV-2 Genome Sequences downloaded from GISAID (1st December 2021): 1,566
Total No. of Sequences Dropped by Nextstrain's Augur Filtering (<27,000 nts): 224
12 had no sequence data
2 of these were dropped because they were in defaults/exclude.txt
34 of these were dropped because of their ambiguous date in any
224 of these were dropped because they were shorter than minimum length of 27,000bp
271 strains were dropped during filtering
1,294 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/v0.4
Genomic Epidemiology of Novel Coronavirus - Pakistan and Related Contextual (Targeted) Samples:
Total no. of Global SARS-CoV-2 Genome Sequences downloaded from GISAID (1st December 2021): 3,434
Total no. of Pakistan SARS-CoV-2 Genome Sequences downloaded from GISAID (1st December 2021): 1,566
Total No. of Sequences that passed all filters: 2,272
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/v0.4
11182021
v0.3.11.18.2021
Genomic Epidemiology of Novel Coronavirus - Pakistan-focused Subsampling (Non-contextual/non-targeted):
Total No. of Pakistan SARS-CoV-2 Genome Sequences downloaded from GISAID (05th November 2021): 1,425
Total No. of Sequences Dropped by Nextstrain's Augur Filtering (<27,000 nts): 241
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/v0.3
Genomic Epidemiology of Novel Coronavirus - Pakistan and Related Contextual (Targeted) Samples:
Total No. of Global SARS-CoV-2 Genome Sequences downloaded from GISAID (8th November 2021): 3,479
Total No. of Pakistan SARS-CoV-2 Genome Sequences downloaded from GISAID (05th November 2021): 1,425
Total No. of Sequences that passed all filters: 2,153
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/v0.3
11052021
v0.2.1.11.05.2021
Genomic Epidemiology of Novel Coronavirus - Pakistan-focused Subsampling (Non-contextual/non-targeted):
Total No. of Pakistan SARS-CoV-2 Genome Sequences downloaded from GISAID (05th November 2021): 1,425
Total No. of Sequences Dropped by Nextstrain's Augur Filtering (<27,000 nts): 241
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/v0.2.1
11052021
v0.2.11.05.2021
Genomic Epidemiology of Novel Coronavirus - Pakistan-focused Subsampling (Non-contextual/non-targeted):
Total No. of Pakistan SARS-CoV-2 Genome Sequences downloaded from GISAID (05th November 2021): 1,425
Total No. of Sequences Dropped by Nextstrain's Augur Filtering (<27,000 nts): 241
Full Change log: https://github.com/AKU-CITRIC-Center-for-Bioinformatics/ncov/commits/v0.2
10212021
v0.1.10.21.2021
Genomic Epidemiology of Novel Coronavirus - Pakistan-focused Subsampling (Non-contextual/non-targeted):
Total No. of Pakistan SARS-CoV-2 Genome Sequences downloaded from GISAID (21st Octrober 2021): 1,109
Total No. of Sequences Dropped by Nextstrain's Augur Filtering (<27,000 nts): 203
Full Change log: https://github.com/AKU-CITRIC-Center-for-Bioinformatics/ncov/commits/v0.1