Nextstrain Discussion

Topic	Replies	Views	Activity
Welcome to nextstrain.discourse.group! General 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…	17	7210	November 14, 2025
SARS-CoV-2 workflow: nextclade.tsv.zst description	2	17	July 10, 2026
Auspice and auspice.us updates Blog	0	17	July 9, 2026
How did you learn Nextstrain when starting from zero? Help and Getting Started	1	21	July 9, 2026
SARS-CoV-2 - no entry in nightly build for RW.1.1.2?	1	48	July 4, 2026
New location for discussion forum General	0	35	June 24, 2026
Criteria for Selecting "Key Mutations" to Define Clades in Augur/Nextstrain Help and Getting Started	2	69	June 24, 2026
Missing nucleotides in entropy output .tsv file Help and Getting Started	1	39	June 23, 2026
Treetime dating - Negative branch lengths	1	65	May 25, 2026
SARS-CoV-2 - no PQ.16.1.1 calls?	2	139	May 25, 2026
Plot augur refine tree with ggtree General	2	91	March 24, 2026
PRRSV1 Reference Dataset General	1	49	March 9, 2026
Include external tools in the Nextstrain Snakemake workflow	3	73	February 6, 2026
How to get the correct time axis when using augur refine and timetree?	4	96	February 4, 2026
SSL error when trying to push Json files to our private group APHA-H5Nx-Avian-Influenza using conda Help and Getting Started	4	73	February 2, 2026
Hosting build on github Help and Getting Started	1	55	January 28, 2026
Incorperating `argur distance` outputs Help and Getting Started	6	515	January 21, 2026
Nextclade short clade annotation H1N1	1	52	January 15, 2026
How to set up next strain	2	54	January 8, 2026
Nextstrain phylogenetic tree in the format used by UCSC General	9	236	December 16, 2025
How do we establish a private mutation threshold for new datasets? General	2	84	December 8, 2025
Reference Dataset Help and Getting Started	1	82	November 10, 2025
Entire recent SARS-CoV-2 batch from Cote d’Ivoire not output from Nextclade CLI Help and Getting Started	4	106	November 6, 2025
Recent comparison of nextclade and pangolin General	1	74	November 4, 2025
Filter for create Dengue phylogenetic tree Help and Getting Started	7	154	November 3, 2025
Measles root sequence Help and Getting Started	5	248	October 29, 2025
Building custom nextclade dataset norovirus Help and Getting Started	7	186	October 17, 2025
Error when trying to download zika pathogen repository Help and Getting Started	1	61	October 14, 2025
Teacher Q on Nextclade RSV-A reference dataset Help and Getting Started	5	104	October 2, 2025
Query about M2-2 gene annotation discrepancy in Nextstrain RSV-A module General	3	94	September 28, 2025