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	969	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	683	June 19, 2020
How to use Nextstrain seasonal flu graph as reference tree for Nextclade?	0	39	September 5, 2023
Displaying a Map in Auspice	2	60	August 22, 2023
Clade Labeling forces AA Mut-file although stated otherwise	2	68	August 21, 2023
Clade difference between influenza HA references	1	112	August 10, 2023
Error message when running Zika tutorial workflow	9	194	July 17, 2023
No release for SARS-CoV-2 May update of nextclade_data?	7	146	June 21, 2023
.meta.genome_annotations failed additionalProperties validation for false	2	141	June 20, 2023
Building frequency plot	1	71	June 13, 2023
Error running ncov-tutorial after fresh install	3	145	May 11, 2023
Is this the expected behaviour of augur tree?	4	136	May 10, 2023
Inconsistencies in the result of augur traits	1	77	May 8, 2023
Zika Index Sequences Error	1	142	May 1, 2023
Ncov: Errors from combine_metadata.py due to unexpected behavior in sanitize_metadata.py	28	470	May 1, 2023
Twice-mutated locations between parent and child lineages	1	172	April 30, 2023
Trouble Installing Nextstrain CLI	7	141	April 29, 2023
GISAID, NCBI or ENA	2	268	April 28, 2023
Access GISAID with NEXTSTRAIN	2	294	April 28, 2023
GISAID account activation help - urgent	2	461	April 28, 2023
Building a Custom Nextstrain - Alignment Error	6	139	April 17, 2023
Intro Event Count	3	145	April 13, 2023
Help for phylogenetic tree about Dengue	15	376	April 6, 2023
Phylogenetic tree dates earlier than root	2	138	April 4, 2023
Creating a dataset with parent-child sequence relations from Auspice tree	7	145	March 23, 2023
How add RBD immune escape score and ACE2 affinity score in the phylogenetics tree	1	193	March 14, 2023
UnicodeDecodeError: 'utf-8' codec can't decode byte 0xa0 in position 1252: invalid start byte	2	541	March 10, 2023
Error in rule align: argument '--jobs'	7	231	February 28, 2023
Augur not found despite having installed Nextstrain CLI	2	151	February 27, 2023
How to add branch labels from node data	1	168	February 23, 2023

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

969

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…