Help and Getting Started

Topic	Replies	Views	Activity
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…	0	970	June 19, 2020
How did you learn Nextstrain when starting from zero?	1	30	July 9, 2026
Criteria for Selecting "Key Mutations" to Define Clades in Augur/Nextstrain	2	97	June 24, 2026
Missing nucleotides in entropy output .tsv file	1	47	June 23, 2026
SSL error when trying to push Json files to our private group APHA-H5Nx-Avian-Influenza using conda	4	95	February 2, 2026
Hosting build on github	1	63	January 28, 2026
Incorperating `argur distance` outputs	6	529	January 21, 2026
Reference Dataset	1	91	November 10, 2025
Entire recent SARS-CoV-2 batch from Cote d’Ivoire not output from Nextclade CLI	4	116	November 6, 2025
Filter for create Dengue phylogenetic tree	7	171	November 3, 2025
Measles root sequence	5	282	October 29, 2025
Building custom nextclade dataset norovirus	7	212	October 17, 2025
Error when trying to download zika pathogen repository	1	66	October 14, 2025
Teacher Q on Nextclade RSV-A reference dataset	5	127	October 2, 2025
Requested color-by field 'num_date' does not exist	3	116	September 25, 2025
Consensus on how to deal with segmented viruses?	5	199	September 22, 2025
Metadata.tsv: building custom nextclade dataset	3	159	August 20, 2025
Accessing geospatial data to map where and when a virus is most common	1	70	August 13, 2025
Xz: command not found	5	155	August 13, 2025
Why the zika tree doesn't include African genotype?	0	35	August 13, 2025
The pipeline takes a very long time to complete	12	192	August 11, 2025
How can I know what columns will be in nextclade output?	11	174	August 5, 2025
Updated Runtime - unable to update CLI and view results	3	69	August 4, 2025
Phylogenetic tree and map of plant viruses	1	110	July 30, 2025
How to display the distribution of lineages on a world map in auspice using the nextstrain build pipeline?	1	83	July 25, 2025
Use the pre-built phylogenetic trees for further analysis	0	56	July 8, 2025
Strain ID and the tab-delimited metadata in Prepare the Sequences	4	168	June 23, 2025
Sequecing data for Africa-Nigeria-Bayelsa	0	65	June 11, 2025
How to use criteria to use data from database (Genbank & GISAID)	0	65	June 11, 2025
Data displayed on nexstrain.org vs downloadable data	2	100	June 5, 2025

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…