01052022 - Omicron Contextuality in Pakistan

v0.6.01.05.2022

Genomic Epidemiology of Novel Coronavirus - Pakistan-focused Subsampling (Non-contextual/non-targeted):

Total no. of Pakistan SARS-CoV-2 Genome Sequences downloaded from GISAID (05th January 2022): 1,701
Total No. of Sequences Dropped by Nextstrain's Augur Filtering (<27000 nts): 267
18 had no sequence data
6 of these were dropped because they were in defaults/exclude.txt
34 of these were dropped because of their ambiguous date in any
267 of these were dropped because they were shorter than minimum length of 27,000bp
284 strains were dropped during filtering
1,383 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/v0.6

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

Total No. of Global SARS-CoV-2 Genome Sequences downloaded from GISAID (05th January 2022): 3,507
Total No. of Pakistan SARS-CoV-2 Genome Sequences downloaded from GISAID (05th January 2022): 1,701
Total No. of Sequences that passed all filters: 2,353

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/v0.6