12072021

v0.4.12.07.2021

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

Total No. of Pakistan SARS-CoV-2 Genome Sequences downloaded from GISAID (1st December 2021): 1,566
Total No. of Sequences Dropped by Nextstrain's Augur Filtering (<27,000 nts): 224
12 had no sequence data
2 of these were dropped because they were in defaults/exclude.txt
34 of these were dropped because of their ambiguous date in any
224 of these were dropped because they were shorter than minimum length of 27,000bp
271 strains were dropped during filtering
1,294 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/v0.4

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

Total no. of Global SARS-CoV-2 Genome Sequences downloaded from GISAID (1st December 2021): 3,434
Total no. of Pakistan SARS-CoV-2 Genome Sequences downloaded from GISAID (1st December 2021): 1,566
Total No. of Sequences that passed all filters: 2,272

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/v0.4