Author: Zhengqiao Zhao; Bahrad A. Sokhansanj; Gail L. Rosen
Title: Characterizing geographical and temporal dynamics of novel coronavirus SARS-CoV-2 using informative subtype markers Document date: 2020_4_9
ID: 9sk11214_1
Snippet: For the aligned sequences, we merged the sequence with the metadata in Nextstrain project 4 as it is in April 6, 2020 based on identification number, gisaid epi isl, provided by GISAID [27] . We further filtered out sequences with incomplete date information in metadata (e.g, "2020-01"), so that our analysis can also incorporate temporal information with daily resolution, given the fast-moving nature of the pandemic. In addition, we filtered out .....
Document: For the aligned sequences, we merged the sequence with the metadata in Nextstrain project 4 as it is in April 6, 2020 based on identification number, gisaid epi isl, provided by GISAID [27] . We further filtered out sequences with incomplete date information in metadata (e.g, "2020-01"), so that our analysis can also incorporate temporal information with daily resolution, given the fast-moving nature of the pandemic. In addition, we filtered out sequences from unknown host or non-human hosts. The resulting final data set contains 3832 sequences excluding the reference sequence. Then, we calculate the entropy by:
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