Help and Getting Started


Topic Replies Views Activity
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…

1 211 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…

2 451 June 19, 2020
Augur tree error from numpy need help to fix
0 10 May 25, 2022
MissingInputException in line 262 of
1 27 May 24, 2022
Strain frequency
4 48 May 18, 2022
Emergent SARS-CoV-2 variants is decreasing
0 19 May 17, 2022
Weekly ECDC variant surveillance data report
0 13 May 17, 2022
GISAID, NCBI or ENA
0 13 May 17, 2022
Error in "main_workflow.smk" file in --latency-wait
7 468 May 16, 2022
My analysis dont show the region from my country
12 58 May 16, 2022
Value error: trying to merge on object and int64 columns
5 41 May 15, 2022
Downloading SARS-CoV-2 data from Nextstrain
1 98 May 14, 2022
Troubleshooting parallelism in Snakemake
0 31 May 8, 2022
Temporality issues : augur refine and Treetime?
2 41 May 5, 2022
Intermediate augur outputs
1 34 May 2, 2022
Error: Alignment must have at least 3 sequences
2 199 May 2, 2022
How to deal with MCC BEAST Tree uncertain data?
2 68 April 29, 2022
Key error in augur export -- `if node["strain"] in node_attrs: KeyError: 'strain'`
2 36 April 27, 2022
Tip_frequencies and tree for 'all' open global_data
1 38 April 19, 2022
Upload more than one fasta on Nexclade Web
1 54 April 14, 2022
Preparing my own data
1 69 April 10, 2022
Nextstrain community builds no dataset available
1 60 April 3, 2022
TreeTime Error: AttributeError: 'NoneType' object has no attribute 'shape'
2 56 April 2, 2022
Treetime Error analysis terminated
2 80 April 2, 2022
WARNING: You asked for a color-by for trait , but it has no values on the tree
4 81 March 28, 2022
Overriding tree builder args
2 68 March 28, 2022
Tip frequencies loading error
14 214 March 23, 2022
Creating tree for genomic subregion(s)
4 74 March 23, 2022
KeyError: UndefinedVariableError: name is not defined
7 76 March 21, 2022
Ncov: how to exclude samples with bad Nextclade QC?
0 62 March 19, 2022