04172023 - BA Contextuality in Pakistan (BA.x spinoffs)

[waqasuddinkhan]

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)

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This discussion was created from the release 04172023 - BA Contextuality in Pakistan (BA.x spinoffs).