Running Bioinformatic Analyses

How-to guides for performing bioinformatic anaylses with Nextstrain.

Table of contents

• Filtering and Subsampling
• Augur and snakemake
• Missing sequence data (gaps, indels, ambiguity)
• Finding a translate and align reference file
• Understanding root and reference sequences
• Importing BEAST MCC trees into augur
• Manually Labeling Clades on a Nextstrain Tree
• Adding Custom Trait Colors
• Adding Custom Lat-Long Data
• Using VCF Input
• Using Fasta Input
• Inferring Sequence Traits (like Drug Resistance)
• Examples of Augur in the wild