01262022 - Omicron Contextuality in Pakistan

[AKU-CITRIC-Center-for-Bioinformatics]

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)

---

This discussion was created from the release 01262022 - Omicron Contextuality in Pakistan.