07192022 - BA Contextuality in Pakistan (BA.x spinoffs)

[waqasuddinkhan]

v1.4.19.06.2022

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 v3.2.4
AUGUR v15.0.2
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 (19th July 2022): 3,240
Total No. of Sequences Dropped by Nextstrain's Augur Filtering (<27000 nts): 587
941 strains were dropped during filtering
344 of these were dropped because they were in results/Pakistan/excluded_by_diagnostics.txt
587 of these were filtered out by the query: "(root_ref == 'yes' & _length >= 27000) | (pakistan == 'yes' & _length >= 27000)"
10 of these were dropped because of their ambiguous date in any
1 strains were added back because they were in defaults/include.txt
2,299 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/v1.4)

Genomic Epidemiology of Novel Coronavirus - Pakistan and Related Contextual (Targeted) Samples:

Total no. of Global SARS-CoV-2 Genome Sequences downloaded from GISAID (19th July 2022): 2,894
Total no. of Pakistan SARS-CoV-2 Genome Sequences downloaded from GISAID (19th July 2022): 3,240
Total No. of Sequences that passed all filters: 2,391

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/v1.4)

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This discussion was created from the release 07192022 - BA Contextuality in Pakistan (BA.x spinoffs).