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	814	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	635	June 19, 2020
Error running ncov-tutorial after fresh install	3	55	May 11, 2023
Is this the expected behaviour of augur tree?	4	63	May 10, 2023
Inconsistencies in the result of augur traits	1	29	May 8, 2023
Zika Index Sequences Error	1	68	May 1, 2023
Ncov: Errors from combine_metadata.py due to unexpected behavior in sanitize_metadata.py	28	314	May 1, 2023
Twice-mutated locations between parent and child lineages	1	83	April 30, 2023
Trouble Installing Nextstrain CLI	7	71	April 29, 2023
GISAID, NCBI or ENA	2	194	April 28, 2023
Access GISAID with NEXTSTRAIN	2	239	April 28, 2023
GISAID account activation help - urgent	2	404	April 28, 2023
Building a Custom Nextstrain - Alignment Error	6	77	April 17, 2023
Intro Event Count	3	76	April 13, 2023
Help for phylogenetic tree about Dengue	15	238	April 6, 2023
Phylogenetic tree dates earlier than root	2	84	April 4, 2023
Error message when running Zika tutorial workflow	2	58	March 27, 2023
Creating a dataset with parent-child sequence relations from Auspice tree	7	96	March 23, 2023
How add RBD immune escape score and ACE2 affinity score in the phylogenetics tree	1	91	March 14, 2023
UnicodeDecodeError: 'utf-8' codec can't decode byte 0xa0 in position 1252: invalid start byte	2	236	March 10, 2023
Error in rule align: argument '--jobs'	7	163	February 28, 2023
Augur not found despite having installed Nextstrain CLI	2	86	February 27, 2023
How to add branch labels from node data	1	109	February 23, 2023
Migration matrix	1	75	February 22, 2023
Discrepancy between Usher and Nextclade lineage calls for mpox	1	58	February 21, 2023
Ancestral sequences	2	102	February 16, 2023
Make Auspice entropy panel show mutations with respect to arbitrary sequence (reference) rather than (reconstructed) root of the tree	2	109	February 15, 2023
Yearly time scale in newick files & leap years	1	78	February 15, 2023
Singularity Image	6	472	February 14, 2023
Custom newick to JSON	8	382	February 8, 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

814

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…