Help and Getting Started


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Guide to filtering GISAID data for division-specific SARS-CoV-2 builds

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…

1 360 March 31, 2022
About the Help and Getting Started category

Whether you’re just getting started or a seasoned expert, this is the place to troubleshoot problems, debug workflows, and puzzle over analyses. If you need or can offer help with Nextstrain, make a new topic in this cat…

2 486 June 19, 2020
Increase weight or colors of transmission lines
1 45 August 4, 2022
Getting node support values in the ncov workflow
2 57 August 4, 2022
Nextclade cli newbie error (windows): Found argument '--input-dataset' which wasn't expected
1 52 July 28, 2022
How to specify what metadata is shown in sample details
2 48 July 27, 2022
Unable to view data on auspice
4 75 July 26, 2022
Spaces in full paths causing problems?
3 48 July 25, 2022
Way to turn off filters?
4 72 July 19, 2022
Error: unknown sequence format for Augur tree
1 44 July 18, 2022
Why does global data for Mexico capture less samples than continental but has a more recent sample than continental [updated]?
0 49 July 15, 2022
SARS-CoV-2 Sequences from Wastewater sample
2 55 July 14, 2022
Error trying to run ncov-tutorial: nextalign2, sanitize_sequences.py
6 79 July 1, 2022
Is there a way to keep the oldest sample among identical sequences?
4 57 June 30, 2022
Augur tree error from numpy need help to fix
1 79 June 30, 2022
Example data results in different phylogeny compared to nextstrain homepage
1 68 June 30, 2022
Split dataset based on timeframe
1 47 June 30, 2022
Problems creating a SARS-CoV-2 BA.5 build
3 64 June 28, 2022
Modification of lines and pie chart
3 63 June 26, 2022
My analysis dont show the region from my country
13 133 June 23, 2022
Cut on borders of tree display
2 52 June 23, 2022
Coloring trees by mutations
2 54 June 21, 2022
Scatterplot S1 mutations from exported data
3 76 June 16, 2022
Subsample Pango lineages in the build file using wildcards?
3 117 June 16, 2022
Tree options layout
2 69 June 16, 2022
Produce "static" auspice visualization for specific dataset
6 106 June 6, 2022
Tutorial data ends up in a tree with 3 seqs only
2 66 June 6, 2022
How to select representative data from GISAID
0 61 June 5, 2022
GISAID, NCBI or ENA
1 61 May 31, 2022
MissingInputException in line 262 of
1 75 May 24, 2022