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	552	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	542	June 19, 2020
My analysis dont show me the especific location that i expect	2	29	November 21, 2022
Zero value for coloring in nextstrain	5	58	November 17, 2022
How do I build a reference genome	0	31	November 14, 2022
Nextclade cli - shortcuts to get just seqName and Nextclade_pango for all recent GISAID samples	2	69	November 14, 2022
Incorperating `argur distance` outputs	4	67	November 8, 2022
Color in emerging lineages	2	73	October 25, 2022
Why do my sequences end up in excluded_by_diagnostics.txt?	3	118	October 18, 2022
Nextclade cli newbie error (windows): Found argument '--input-dataset' which wasn't expected	2	140	October 15, 2022
Is there any way to locally view the result like clades.nextstrain.org?	8	191	September 20, 2022
Where can I look up clade defining mutations for seasonal flu?	0	80	August 31, 2022
Obtain numerical values on the transmission between countries	3	125	September 6, 2022
Error in jobid: 22	0	42	September 5, 2022
How to visualize result	1	89	September 1, 2022
Error: Alignment must have at least 3 sequences	3	315	August 31, 2022
Windows 10 won't install Nextclade CLI	2	113	August 19, 2022
Increase weight or colors of transmission lines	1	117	August 4, 2022
Getting node support values in the ncov workflow	2	127	August 4, 2022
How to specify what metadata is shown in sample details	2	104	July 27, 2022
Unable to view data on auspice	4	159	July 26, 2022
Spaces in full paths causing problems?	3	111	July 25, 2022
Way to turn off filters?	4	141	July 19, 2022
Error: unknown sequence format for Augur tree	1	105	July 18, 2022
Why does global data for Mexico capture less samples than continental but has a more recent sample than continental [updated]?	0	111	July 15, 2022
SARS-CoV-2 Sequences from Wastewater sample	2	118	July 14, 2022
Error trying to run ncov-tutorial: nextalign2, sanitize_sequences.py	6	151	July 1, 2022
Is there a way to keep the oldest sample among identical sequences?	4	102	June 30, 2022
Augur tree error from numpy need help to fix	1	130	June 30, 2022
Example data results in different phylogeny compared to nextstrain homepage	1	113	June 30, 2022

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

552

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…