Online Tools - Resource for Coronavirus 2019

Haplotype

The haplotype network will be constructed via McAN (minimum-cost arborescence-based haplotype network). Please upload SARS-CoV-2 sequence mutations (in customized genovar format, .gf or vcf.gz) and the corresponding metadata, select a specific dataset from Resource for Coronavirus 2019 (RCoV19), or combined both of them. You can select a specific dataset by filtering sampling time, or sampling locations etc., or by sampling randomly in RCoV19. Based on constructed haplotype network, community lineages will be determined by Newman’s method. Note that mutations in the 3’UTR and 5’UTR will be filtered out.

Select File Format

Mutation file format

VCF file format

Upload mutation file

Upload meta file

Start sampling date

End sampling date

Country

Missing sampling date type

Random sampling count(recommend 0 < N < 10000)

Minimum mutation rate(for selecting high-mutational-rate sites)

Subject

Run

Reminder: Running tasks: , Tasks in queue: .

1. Input File Format Description

a) Metadata and mutations are needed for constructing haplotype network and assigning community lineages.
b) In mutation file, each row contains the mutation information including virus strain name, accession ID, and mutations split by ‘\t’ in genovariations format (GF).
c) In metadata file, each row contains the meta information of a sample including accession ID, sampling time (yyyy-mm-dd or yyyy-mm), and sampling location (country), which is split by ‘\t’.

2. Mutation Example

Name	Accession	Mutations
hCoV-19/human/USA/TX-DSHS-000508/2020	EPI_ISL_2264424	490(SNP:T->A);3177(SNP:C->T);6040(SNP:C->T);6843(SNP:C->T);8782(SNP:C->T);8950(SNP:C->T);12478(SNP:G->A);18736(SNP:T->C);24034(SNP:C->T);26729(SNP:T->C);26801(SNP:C->T);28077(SNP:G->C);28144(SNP:T->C);28896(SNP:C->G);29451(SNP:C->T);29700(SNP:A->G)
hCoV-19/human/USA/TX-DSHS-000511/2020	EPI_ISL_2264432	3003(SNP:A->T);8782(SNP:C->T);10811(SNP:C->T);10813(SNP:T->A);17747(SNP:C->T);17858(SNP:A->G);18060(SNP:C->T);24694(SNP:A->T);28144(SNP:T->C)
hCoV-19/human/USA/TX-DSHS-000513/2020	EPI_ISL_2264434	3003(SNP:A->T);8782(SNP:C->T);10811(SNP:C->T);10813(SNP:T->A);17747(SNP:C->T);17858(SNP:A->G);18060(SNP:C->T);24694(SNP:A->T);28144(SNP:T->C)
hCoV-19/human/USA/TX-DSHS-000515/2020	EPI_ISL_2264437	241(SNP:C->T);3037(SNP:C->T);8664(SNP:C->T);14408(SNP:C->T);15026(SNP:C->T);15264(SNP:T->C);23403(SNP:A->G);27575(SNP:C->T)
hCoV-19/human/USA/TX-DSHS-000502/2020	EPI_ISL_2264410	241(SNP:C->T);1059(SNP:C->T);3037(SNP:C->T);3068(SNP:G->A);9169(SNP:C->T);14408(SNP:C->T);23403(SNP:A->G);25563(SNP:G->T)

3. Meta Example

Accession	Sampling Date	Sampling Location
EPI_ISL_2249479	2020-04-13	United States
EPI_ISL_2254726	2020-04-24	Slovakia
EPI_ISL_2270090	2020-05-11	Switzerland
EPI_ISL_2274027	2020-05-14	Haiti
EPI_ISL_2278820	2020-04-27	Sweden