# Latest **URL:** https://nextstrain.discourse.group/latest.md?page=1 [Latest](https://nextstrain.discourse.group/latest.md) · [Categories](https://nextstrain.discourse.group/categories.md) **Page:** 2 --- ## [Building custom nextclade dataset norovirus](https://nextstrain.discourse.group/t/building-custom-nextclade-dataset-norovirus/2000)
**Author:** [@qianlw](https://nextstrain.discourse.group/u/qianlw)\ **Replies:** 7\ **Last updated:** [October 17, 2025, 4:46pm UTC](https://nextstrain.discourse.group/t/building-custom-nextclade-dataset-norovirus/2000 "2025-10-17T16:46:16Z")
I tried build custom dataset norovirus following the tutorials from https://github.com/nextstrain/nextclade\_data/blob/master/docs/dataset-creation-guide.md., when creating a reference tree using Snakefile, not just desc… --- ## [Error when trying to download zika pathogen repository](https://nextstrain.discourse.group/t/error-when-trying-to-download-zika-pathogen-repository/1999)
**Author:** [@lucindaG](https://nextstrain.discourse.group/u/lucindaG)\ **Replies:** 1\ **Last updated:** [October 14, 2025, 12:20pm UTC](https://nextstrain.discourse.group/t/error-when-trying-to-download-zika-pathogen-repository/1999 "2025-10-14T12:20:42Z")
Good Day I am trying to download the zika pathogen repository. I have successfully managed to download Nextstrain, Augur and Auspice; however, I get an error after pasting ‘ git clone https://github.com/nextstrain/zika-… --- ## [Teacher Q on Nextclade RSV-A reference dataset](https://nextstrain.discourse.group/t/teacher-q-on-nextclade-rsv-a-reference-dataset/1998)
**Author:** [@Achattwood](https://nextstrain.discourse.group/u/Achattwood)\ **Replies:** 5\ **Last updated:** [October 2, 2025, 5:18pm UTC](https://nextstrain.discourse.group/t/teacher-q-on-nextclade-rsv-a-reference-dataset/1998 "2025-10-02T17:18:00Z")
Note: I know next to nothing about bioinformatics I am a teacher that used the Nextclade RSV-A reference dataset as part of a classroom activity for Gr.11 students. The activity relied on the four nucleotide sequences l… --- ## [Query about M2-2 gene annotation discrepancy in Nextstrain RSV-A module](https://nextstrain.discourse.group/t/query-about-m2-2-gene-annotation-discrepancy-in-nextstrain-rsv-a-module/1962)
**Author:** [@yangjq](https://nextstrain.discourse.group/u/yangjq)\ **Replies:** 3\ **Last updated:** [September 28, 2025, 8:33am UTC](https://nextstrain.discourse.group/t/query-about-m2-2-gene-annotation-discrepancy-in-nextstrain-rsv-a-module/1962 "2025-09-28T08:33:42Z")
Dear Nextstrain Team, I hope this message finds you well. I am writing to seek clarification regarding the annotation of the M2-2 gene in the RSV-A module on Nextstrain. I noticed a discrepancy between the M2-2 gene co… --- ## [Requested color-by field 'num\_date' does not exist](https://nextstrain.discourse.group/t/requested-color-by-field-num-date-does-not-exist/1997)
**Author:** [@eam](https://nextstrain.discourse.group/u/eam)\ **Replies:** 3\ **Last updated:** [September 25, 2025, 6:50pm UTC](https://nextstrain.discourse.group/t/requested-color-by-field-num-date-does-not-exist/1997 "2025-09-25T18:50:32Z")
Hello! I am loving Nextstrain and currently attempting to create pathogen repositories for two poultry-related viruses. For one of the viruses, I was able to successfully run the default pathogen-repo-guide ingest workfl… --- ## [Consensus on how to deal with segmented viruses?](https://nextstrain.discourse.group/t/consensus-on-how-to-deal-with-segmented-viruses/1994)
**Author:** [@eam](https://nextstrain.discourse.group/u/eam)\ **Replies:** 5\ **Last updated:** [September 22, 2025, 6:10pm UTC](https://nextstrain.discourse.group/t/consensus-on-how-to-deal-with-segmented-viruses/1994 "2025-09-22T18:10:23Z")
I’m attempting to create a new pathogen repo using the steps laid out on the Nextstrain website. I’ve successfully run the default ingest workflow for my pathogen with a few minor modifications (adding in some columns). … --- ## [Mistakes in the country label of some zika samples？](https://nextstrain.discourse.group/t/mistakes-in-the-country-label-of-some-zika-samples/1978)
**Author:** [@pangmingfan](https://nextstrain.discourse.group/u/pangmingfan)\ **Replies:** 5\ **Last updated:** [September 4, 2025, 12:37am UTC](https://nextstrain.discourse.group/t/mistakes-in-the-country-label-of-some-zika-samples/1978 "2025-09-04T00:37:14Z")
I noticed some discrepancies in the country labels of Zika samples. For example, in Figure 1, two samples uploaded by China were incorrectly labeled as Venezuela（Z16019 and GZ02/2016）. In Figure 2, multiple samples from … --- ## [Filter parameters for all-time global SARS-CoV-2 dataset](https://nextstrain.discourse.group/t/filter-parameters-for-all-time-global-sars-cov-2-dataset/1992)
**Author:** [@diegogotex](https://nextstrain.discourse.group/u/diegogotex)\ **Replies:** 2\ **Last updated:** [August 22, 2025, 11:10am UTC](https://nextstrain.discourse.group/t/filter-parameters-for-all-time-global-sars-cov-2-dataset/1992 "2025-08-22T11:10:03Z")
Hi all, I’m using the SARS-CoV-2 all-time global dataset ( auspice ) to generate a small tree by adding some new samples. Is there any documentation available about the filters that are applied to generate the sets for… --- ## [Metadata.tsv: building custom nextclade dataset](https://nextstrain.discourse.group/t/metadata-tsv-building-custom-nextclade-dataset/1980)
**Author:** [@AnnaN](https://nextstrain.discourse.group/u/AnnaN)\ **Replies:** 3\ **Last updated:** [August 20, 2025, 6:20pm UTC](https://nextstrain.discourse.group/t/metadata-tsv-building-custom-nextclade-dataset/1980 "2025-08-20T18:20:39Z")
Hi! I’m in the process of building a custom dataset in the nextclade\_data repo, and have now reached the point of tree building with the snakefile provided in example-workflow. I want to hand select the genomes to go int… --- ## [Accessing geospatial data to map where and when a virus is most common](https://nextstrain.discourse.group/t/accessing-geospatial-data-to-map-where-and-when-a-virus-is-most-common/1977)
**Author:** [@Sauron](https://nextstrain.discourse.group/u/Sauron)\ **Replies:** 1\ **Last updated:** [August 13, 2025, 5:58pm UTC](https://nextstrain.discourse.group/t/accessing-geospatial-data-to-map-where-and-when-a-virus-is-most-common/1977 "2025-08-13T17:58:11Z")
I’m new to this platform and working on a small project involving epidemiological data. Is there a function, or mode that can provide geospatial data showing the prevalence of a virus in different areas of a country at a… --- ## [Xz: command not found](https://nextstrain.discourse.group/t/xz-command-not-found/1969)
**Author:** [@NikitaSitharam](https://nextstrain.discourse.group/u/NikitaSitharam)\ **Replies:** 5\ **Last updated:** [August 13, 2025, 5:11pm UTC](https://nextstrain.discourse.group/t/xz-command-not-found/1969 "2025-08-13T17:11:47Z")
Hi Nextstrain Team, I am trying to run the ncov pipeline with my own reference and custom data which was downloaded from GISAID in the Augur format. I have previously run this workflow before when there were different y… --- ## [Why the zika tree doesn't include African genotype?](https://nextstrain.discourse.group/t/why-the-zika-tree-doesnt-include-african-genotype/1979)
**Author:** [@pangmingfan](https://nextstrain.discourse.group/u/pangmingfan)\ **Replies:** 0\ **Last updated:** [August 13, 2025, 6:54am UTC](https://nextstrain.discourse.group/t/why-the-zika-tree-doesnt-include-african-genotype/1979 "2025-08-13T06:54:39Z")
I noticed that the Nextstrain zika tree only inlude Asian genotype samples, with the earliest sample from Thailand in 2013. Why the African genotype samples weren’t there? Is it because of the poor quality of African sam… --- ## [The pipeline takes a very long time to complete](https://nextstrain.discourse.group/t/the-pipeline-takes-a-very-long-time-to-complete/1946)
**Author:** [@magletdinov](https://nextstrain.discourse.group/u/magletdinov)\ **Replies:** 12\ **Last updated:** [August 11, 2025, 7:17pm UTC](https://nextstrain.discourse.group/t/the-pipeline-takes-a-very-long-time-to-complete/1946 "2025-08-11T19:17:38Z")
Good afternoon! I am running the classic ncov pipeline on my own data (300 genomes) and on https://data.nextstrain.org/files/ncov/open/global/sequences.fasta.xz as a reference. Please tell me, is it normal for the pipel… --- ## [Chikungunya Virus, 250 years old?](https://nextstrain.discourse.group/t/chikungunya-virus-250-years-old/1967)
**Author:** [@jiehuang001](https://nextstrain.discourse.group/u/jiehuang001)\ **Replies:** 3\ **Last updated:** [August 10, 2025, 6:39pm UTC](https://nextstrain.discourse.group/t/chikungunya-virus-250-years-old/1967 "2025-08-10T18:39:00Z")
Hi, there: I downloaded the high-depth sequence data for 4,590 Chikungunya Virus from GISAID, and run a nextstrain analysis. Please see the screenshot below. I am so surprised to see that the inferred root of the phylog… --- ## [How can I know what columns will be in nextclade output?](https://nextstrain.discourse.group/t/how-can-i-know-what-columns-will-be-in-nextclade-output/1934)
**Author:** [@pvanheus](https://nextstrain.discourse.group/u/pvanheus)\ **Replies:** 11\ **Last updated:** [August 5, 2025, 9:39am UTC](https://nextstrain.discourse.group/t/how-can-i-know-what-columns-will-be-in-nextclade-output/1934 "2025-08-05T09:39:10Z")
I am trying to update the Galaxy wrapper for nextclade. The current (very outdated) wrapper maps dataset name to column names to use in the output and producing this list was a manual process. So: is there a way to compu… --- ## [Updated Runtime - unable to update CLI and view results](https://nextstrain.discourse.group/t/updated-runtime-unable-to-update-cli-and-view-results/1968)
**Author:** [@NyxMoiren](https://nextstrain.discourse.group/u/NyxMoiren)\ **Replies:** 3\ **Last updated:** [August 4, 2025, 6:56pm UTC](https://nextstrain.discourse.group/t/updated-runtime-unable-to-update-cli-and-view-results/1968 "2025-08-04T18:56:59Z")
Hello! I have updated the runtime and now wanted to update the CLI. Analysis runs successfully, but when I want to view it with nextstrain view . I get an 404 error. When I want to update the CLI with conda instal… --- ## [Negative Dates in Auspice Timeline When Using YY-XX-XX Format](https://nextstrain.discourse.group/t/negative-dates-in-auspice-timeline-when-using-yy-xx-xx-format/1964)
**Author:** [@Komal](https://nextstrain.discourse.group/u/Komal)\ **Replies:** 1\ **Last updated:** [August 4, 2025, 6:46pm UTC](https://nextstrain.discourse.group/t/negative-dates-in-auspice-timeline-when-using-yy-xx-xx-format/1964 "2025-08-04T18:46:08Z")
Hi, I’m encountering an issue where the Auspice timeline displays large negative date values (e.g., -89900). In my metadata file, the date column is formatted as YY-XX-XX - for example, 26-XX-XX for the year 2026 with u… --- ## [Inconsistent QC Results Between Nextclade CLI and Web Version](https://nextstrain.discourse.group/t/inconsistent-qc-results-between-nextclade-cli-and-web-version/1966)
**Author:** [@georges.hanna](https://nextstrain.discourse.group/u/georges.hanna)\ **Replies:** 2\ **Last updated:** [August 4, 2025, 11:49am UTC](https://nextstrain.discourse.group/t/inconsistent-qc-results-between-nextclade-cli-and-web-version/1966 "2025-08-04T11:49:37Z")
Hello everyone, I’m working with a SARS-CoV-2 dataset and trying to filter sequences based on qc.overallStatus using Nextclade. When I run Nextclade via the command line, all my sequences are labeled with “good” qualit… --- ## [Phylogenetic tree and map of plant viruses](https://nextstrain.discourse.group/t/phylogenetic-tree-and-map-of-plant-viruses/1939)
**Author:** [@amir1461](https://nextstrain.discourse.group/u/amir1461)\ **Replies:** 1\ **Last updated:** [July 30, 2025, 12:37am UTC](https://nextstrain.discourse.group/t/phylogenetic-tree-and-map-of-plant-viruses/1939 "2025-07-30T00:37:31Z")
Subject: Request for Assistance in Building Phylogenetic Tree and Map for Plant Virus Sequences Dear Nextstrain Team, I hope this message finds you well. My name is Amir, and I am currently working on a research proje… --- ## [How to display the distribution of lineages on a world map in auspice using the nextstrain build pipeline?](https://nextstrain.discourse.group/t/how-to-display-the-distribution-of-lineages-on-a-world-map-in-auspice-using-the-nextstrain-build-pipeline/1937)
**Author:** [@magletdinov](https://nextstrain.discourse.group/u/magletdinov)\ **Replies:** 1\ **Last updated:** [July 25, 2025, 4:49pm UTC](https://nextstrain.discourse.group/t/how-to-display-the-distribution-of-lineages-on-a-world-map-in-auspice-using-the-nextstrain-build-pipeline/1937 "2025-07-25T16:49:21Z")
Good afternoon! I am trying to run the ncov pipeline, but for some reason I do not see a world map with my samples in the results. I have added all the necessary information (region, country, division, location) to the c… --- ## [Use the pre-built phylogenetic trees for further analysis](https://nextstrain.discourse.group/t/use-the-pre-built-phylogenetic-trees-for-further-analysis/1924)
**Author:** [@pangmingfan](https://nextstrain.discourse.group/u/pangmingfan)\ **Replies:** 0\ **Last updated:** [July 8, 2025, 3:13am UTC](https://nextstrain.discourse.group/t/use-the-pre-built-phylogenetic-trees-for-further-analysis/1924 "2025-07-08T03:13:31Z")
Hello everyone! I’m very interested in the Zika virus results provided by Nextstrain. I plan to use the pre-built phylogenetic trees for further in-depth analysis, focusing on: Global cross-border transmission routes an… --- ## [H1N1 pdm09 tree - EPI ISL identifiers](https://nextstrain.discourse.group/t/h1n1-pdm09-tree-epi-isl-identifiers/1921)
**Author:** [@georges.hanna](https://nextstrain.discourse.group/u/georges.hanna)\ **Replies:** 1\ **Last updated:** [June 26, 2025, 11:04pm UTC](https://nextstrain.discourse.group/t/h1n1-pdm09-tree-epi-isl-identifiers/1921 "2025-06-26T23:04:45Z")
I’m trying to download the acknowledgments for the H1N1pdm09 (seasonal influenza) dataset from Nextstrain. However, I can only see the virus names — the EPI\_ISL identifiers for the sequences are not available. I need to … --- ## [Strain ID and the tab-delimited metadata in Prepare the Sequences](https://nextstrain.discourse.group/t/strain-id-and-the-tab-delimited-metadata-in-prepare-the-sequences/1918)
**Author:** [@YAOsanmeme](https://nextstrain.discourse.group/u/YAOsanmeme)\ **Replies:** 4\ **Last updated:** [June 23, 2025, 5:31pm UTC](https://nextstrain.discourse.group/t/strain-id-and-the-tab-delimited-metadata-in-prepare-the-sequences/1918 "2025-06-23T17:31:41Z")
I’m a newbie who is just getting started. I’ve already completed the steps of installing and running a phylogenetic workflow., However I’m now stuck at the “Prepare the Sequences” step. The sequence I downloaded from the… --- ## [Need new reference sequences for SARS-CoV2?](https://nextstrain.discourse.group/t/need-new-reference-sequences-for-sars-cov2/1896)
**Author:** [@LPI](https://nextstrain.discourse.group/u/LPI)\ **Replies:** 1\ **Last updated:** [June 15, 2025, 5:16pm UTC](https://nextstrain.discourse.group/t/need-new-reference-sequences-for-sars-cov2/1896 "2025-06-15T17:16:03Z")
Hello, It’s been a while since I last used Nextclade, and a majority of the sequences I’ve submitted for samples taken between January and April 2025 show a very high number of mutations. The reference sequence used is … --- ## [RSV-A Reference Sequence Question](https://nextstrain.discourse.group/t/rsv-a-reference-sequence-question/1908)
**Author:** [@T4R4](https://nextstrain.discourse.group/u/T4R4)\ **Replies:** 2\ **Last updated:** [June 13, 2025, 2:20pm UTC](https://nextstrain.discourse.group/t/rsv-a-reference-sequence-question/1908 "2025-06-13T14:20:10Z")
Hello, I noticed that the referenced RSV-A NCBI accession has been updated to the INSDC reference that differs slightly from the A/England/397/2017 reference used in the RSV-A Nextclade dataset. I was wondering if there… --- ## [Sequecing data for Africa-Nigeria-Bayelsa](https://nextstrain.discourse.group/t/sequecing-data-for-africa-nigeria-bayelsa/1907)
**Author:** [@richardagedah](https://nextstrain.discourse.group/u/richardagedah)\ **Replies:** 0\ **Last updated:** [June 11, 2025, 2:48pm UTC](https://nextstrain.discourse.group/t/sequecing-data-for-africa-nigeria-bayelsa/1907 "2025-06-11T14:48:34Z")
Hi everyone, i am Richard. Pls, i need help. i downloaded data for Africa-Nigeria-Bayelsa for covid-19, with 22 sequencing data. I am struggling to get the 22 individual sequences to blast them on the NCBI web site. can … --- ## [How to use criteria to use data from database (Genbank & GISAID)](https://nextstrain.discourse.group/t/how-to-use-criteria-to-use-data-from-database-genbank-gisaid/1905)
**Author:** [@Soon\_tare](https://nextstrain.discourse.group/u/Soon_tare)\ **Replies:** 0\ **Last updated:** [June 11, 2025, 5:37am UTC](https://nextstrain.discourse.group/t/how-to-use-criteria-to-use-data-from-database-genbank-gisaid/1905 "2025-06-11T05:37:40Z")
I have question about criteria to retrieve information from both database (Genbank & GISAID) , hope every user may help me to explain in detail T^T thanks you so much --- ## [Data displayed on nexstrain.org vs downloadable data](https://nextstrain.discourse.group/t/data-displayed-on-nexstrain-org-vs-downloadable-data/1902)
**Author:** [@samf](https://nextstrain.discourse.group/u/samf)\ **Replies:** 2\ **Last updated:** [June 5, 2025, 7:22am UTC](https://nextstrain.discourse.group/t/data-displayed-on-nexstrain-org-vs-downloadable-data/1902 "2025-06-05T07:22:21Z")
Hello, Thank you for all the amazing work you do ! I recently downloaded the dengue data from Nextstrain (https://data.nextstrain.org/files/workflows/dengue/sequences\_all.fasta.zst). The number of sequences there is ar… --- ## [How can one identify host-adaptive/associated mutations from a tree?](https://nextstrain.discourse.group/t/how-can-one-identify-host-adaptive-associated-mutations-from-a-tree/1899)
**Author:** [@ankeetkumar](https://nextstrain.discourse.group/u/ankeetkumar)\ **Replies:** 0\ **Last updated:** [May 25, 2025, 10:53am UTC](https://nextstrain.discourse.group/t/how-can-one-identify-host-adaptive-associated-mutations-from-a-tree/1899 "2025-05-25T10:53:02Z")
Dear all, I want to identify host-adaptive/associated mutations from sequence data. Can I get guidance on this? Thanks --- ## [Mapbox display issue (api changing without building auspice)](https://nextstrain.discourse.group/t/mapbox-display-issue-api-changing-without-building-auspice/1887)
**Author:** [@mhananda](https://nextstrain.discourse.group/u/mhananda)\ **Replies:** 3\ **Last updated:** [May 12, 2025, 9:13pm UTC](https://nextstrain.discourse.group/t/mapbox-display-issue-api-changing-without-building-auspice/1887 "2025-05-12T21:13:48Z")
Hello, Is there any way to update the mapbox api for the auspice without building it? I want to display the map to the global viewers (not localhost) but i don’t want to build the auspice, just use view. Thanks! [Previous page](https://nextstrain.discourse.group/latest.md) [Next page](https://nextstrain.discourse.group/latest.md?page=2)