Haplotype Explorer

HaplotypeExplorer is an interactive haplotype network viewer for spatiotemporal dissection of multimodal epidemic spectra.

How to start

• Click green button "↓Code" and download files.
• To see example results, open Example.
• To visualize your data in Haplotype Explorer, run python createHTML.py after preparing input.fasta and installing dependencies.

Contents of Example

• Example networks, JSON files, and a movie are available in Example. Please look after download by pressing green button "↓Code".
  • html files: Example outputs of Haplotype Explorer. Please open it in a browser after saving as a HTML file.
  • json files: Users can share and resume the network by input JSON into Haplotype Explorer. Please see manual.pdf.
  • movie: The movie depicting the eruption of the SARS-CoV-2 in the world from 2019 DEC 31 to 2020 MAR 21.

How to visualize your data

The way to visualize users data is also described in Figure 2. Please see also manual.pdf.

• Install dependencies with conda: conda install -c bioconda seqkit mafft cd-hit snp-sites trimal
  • If you have no permission to access /usr/local/, you will need to specify another path with --prefix when you run conda.
• Put multi-FASTA as input.fasta and run python createHTML.py
• result.html will automatically open after calculation.

Requirements

• We confirmed compatibilities of Haplotype Explorer and the bundled python scripts with the latest versions of Safari, Firefox, Edge, Chrome, and Python3 on macOS Catalina 10.15.3, respectively.

Limitation

Sequence amount, SNV length, and genetic distance among inputs will affect calculation time and result.

• The TCS requires several hours for a few thousands sequences/SNVs (in standard iMac). Alignment also takes a long time for a large input.
• It also splits the network automatically when inputs have too long genetic distance.
• Using over thousands of sequences make it difficult to visualize the result due to multiple edges.
• Also, it does not consider sequence gaps, recombination, and reassortment.

Therefore, we recommend:

• start with a small set and gradually scale up until you can obtain a reasonable result.
• use < 500 haplotypes and < 3000 SNVs in case of SARS-CoV-2 (due to calculation time and quality of the result of TCS).
• analyze separately for long distance input

Citation

Tetsuro Kawano-Sugaya1*, Koji Yatsu1, Tsuyoshi Sekizuka1, Kentaro Itokawa1, Masanori Hashino1, Rina Tanaka1, Makoto Kuroda1 (2020)
Haplotype Explorer: infection cluster visualization tool toward spatiotemporal dissection of the COVID-19 pandemic.
bioRxiv. doi: https://www.biorxiv.org/content/10.1101/2020.07.19.179101v1

1 Pathogen Genomics Center, National Institute of Infectious Diseases, Toyama 1-23-1, Shinjuku, Tokyo, Japan
* Corresponding author: Tetsuro Kawano-Sugaya (tks_jp@seikai.org)