Enhancement ideas

nextflu enhancements

• passage associations: could simply test for association between aa and "orig/clinial"
• count # of times a site was hit by mutation in recent years
• site with all HI strains in parallel to site with even geo rep
• include larger number of sequences, introduce weights to even out NA oversampling
• age and gender is available in GISAID for most CDC samples -> could be exported and displayed ​ ​

big nextflu items

• include other segments, link multiple trees
• reassortment analysis ​​

database

• fix lack of old sequences and titers
• direct integration of database download into augur pipeline
• include all 8 segments
• maybe xls export would be more flexible than fasta ​ ​

prediction

• proper integration of cHI
• automated reports? ​* list of clades (mutations) of concern
• snapshots important --- provide nextflu "freeze" along with report

priority queue

1. Geographic distribution and sample count
2. Hopeful monsters (flag mutations and measure clade growth)
3. Passage mutations (tooltip listing passage, coloring option)
4. HI enriched site
5. Incorporate neutralization assays (maybe with a scaling, validate titers)
6. Egg culture