10212022 - BA Contextuality in Pakistan (BA.x spinoffs)

[waqasuddinkhan]

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)

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This discussion was created from the release 10212022 - BA Contextuality in Pakistan (BA.x spinoffs).