03302022 - Omicron Contextuality in Pakistan

[AKU-CITRIC-Center-for-Bioinformatics]

v1.0.03.30.2022

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 v3.0.6
AUGUR v14.0.0
IQ-TREE multicore v2.2.0-beta COVID-edition for Linux 64-bit built Dec 21 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 (30th March 2022): 2,128
Total No. of Sequences Dropped by Nextstrain's Augur Filtering (<27000 nts): 313
663 strains were dropped during filtering
342 of these were dropped because they were in results/Pakistan/excluded_by_diagnostics.txt
313 of these were filtered out by the query: "(root_ref == 'yes' & _length >= 27000) | (pakistan == 'yes' & _length >= 27000)"
8 of these were dropped because of their ambiguous date in any
3 strains were added back because they were in defaults/include.txt
1,465 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/v1.0)

Genomic Epidemiology of Novel Coronavirus - Pakistan and Related Contextual (Targeted) Samples:
Total no. of Pakistan SARS-CoV-2 Genome Sequences downloaded from GISAID (30th March 2022): 2,128
Total no. of Global SARS-CoV-2 Genome Sequences downloaded from GISAID (30th March 2022): 2,917
Total No. of Sequences that passed all filters: 2,441

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/v1.0)

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This discussion was created from the release 03302022 - Omicron Contextuality in Pakistan.