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	714	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	599	June 19, 2020
Error message when running Zika tutorial workflow	2	23	March 27, 2023
Help for phylogenetic tree about Dengue	13	124	March 23, 2023
Creating a dataset with parent-child sequence relations from Auspice tree	7	52	March 23, 2023
Phylogenetic tree dates earlier than root	1	37	March 21, 2023
How add RBD immune escape score and ACE2 affinity score in the phylogenetics tree	1	33	March 14, 2023
UnicodeDecodeError: 'utf-8' codec can't decode byte 0xa0 in position 1252: invalid start byte	2	63	March 10, 2023
Error in rule align: argument '--jobs'	7	111	February 28, 2023
Augur not found despite having installed Nextstrain CLI	2	56	February 27, 2023
How to add branch labels from node data	1	61	February 23, 2023
Migration matrix	1	42	February 22, 2023
Discrepancy between Usher and Nextclade lineage calls for mpox	1	30	February 21, 2023
Ancestral sequences	2	72	February 16, 2023
Make Auspice entropy panel show mutations with respect to arbitrary sequence (reference) rather than (reconstructed) root of the tree	2	69	February 15, 2023
Yearly time scale in newick files & leap years	1	51	February 15, 2023
Singularity Image	6	421	February 14, 2023
Custom newick to JSON	8	309	February 8, 2023
Downloading newick versions programatically	4	57	January 27, 2023
Sites to ignore for Omicron tree building	0	116	January 26, 2023
Samples in json vs newick files, & branch lengths	2	63	January 24, 2023
Is the default IQtree parameter usually good enough?	0	52	January 17, 2023
Auspice view fails to load the datasets	2	70	January 16, 2023
Nextclade cli - shortcuts to get just seqName and Nextclade_pango for all recent GISAID samples	7	209	January 14, 2023
seqName format different between GISAID FASTA All sequences package vs search results	2	95	January 14, 2023
Broken workflow after updating runtime and CLI	3	95	December 15, 2022
Some African Countries (Burkina Faso, Sierra Leone) Build failed	2	82	December 12, 2022
My analysis dont show me the especific location that i expect	2	104	November 21, 2022
Zero value for coloring in nextstrain	5	116	November 17, 2022
How do I build a reference genome	0	96	November 14, 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

714

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…