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Guide to filtering GISAID data for division-specific SARS-CoV-2 builds
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Background One common use case for SARS-CoV-2 analyses is to create a phylogeny focused on a specific place and time with contextual sequences that are genetically related to sequences in the focal region. Although it’s…

1 210 March 31, 2022
Welcome to discussion.nextstrain.org!
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This website is intended to be a community forum for people using Nextstrain. We’re very interested to help public health and academic groups run Nextstrain analyses and share them (publicly or privately). The goal is to…

8 2407 June 2, 2021
Map not displayed completely
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9 34 May 26, 2022
Augur tree error from numpy need help to fix
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0 9 May 25, 2022
MissingInputException in line 262 of
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1 26 May 24, 2022
Strain frequency
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4 46 May 18, 2022
Losing country info in final build
General
4 53 May 17, 2022
Emergent SARS-CoV-2 variants is decreasing
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0 19 May 17, 2022
Weekly ECDC variant surveillance data report
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0 13 May 17, 2022
GISAID, NCBI or ENA
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0 13 May 17, 2022
Relating the Phylogenetic Tree result to a Transmission Tree of Infectious Disease Outbreaks
1 40 May 17, 2022
Error in "main_workflow.smk" file in --latency-wait
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7 467 May 16, 2022
Clock Deviation
0 19 May 16, 2022
My analysis dont show the region from my country
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12 56 May 16, 2022
Value error: trying to merge on object and int64 columns
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5 40 May 15, 2022
Downloading SARS-CoV-2 data from Nextstrain
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1 98 May 14, 2022
Troubleshooting parallelism in Snakemake
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0 30 May 8, 2022
Contextual strain list from augur filter
General
0 24 May 6, 2022
Import Beast tree
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4 44 May 6, 2022
KeyError: 'Nextclade_pango' in ncov build
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7 66 May 5, 2022
Temporality issues : augur refine and Treetime?
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2 41 May 5, 2022
Pango lineage (Nextclade)
General
2 74 May 2, 2022
GISAID - nextclade designations?
1 69 May 2, 2022
Intermediate augur outputs
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1 31 May 2, 2022
Error: Alignment must have at least 3 sequences
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2 198 May 2, 2022
How to deal with MCC BEAST Tree uncertain data?
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2 65 April 29, 2022
Key error in augur export -- `if node["strain"] in node_attrs: KeyError: 'strain'`
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2 32 April 27, 2022
Export transmission lines
General
4 108 April 24, 2022
Tip_frequencies and tree for 'all' open global_data
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1 38 April 19, 2022
Upload more than one fasta on Nexclade Web
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1 52 April 14, 2022