This is a website I build to track Salmonella outbreak using genomic data.
The bioinformatics pipeline included the following main steps:
- Align FASTQ files to the reference genome with BWA
- Sort BAM files with Samtools
- Call SNPs with BCFtools
- Annotate SNPs with BCFtools (and GFF and GenBank files)
- Infer phylogeny with FastTree/IQ-Tree
- Develop Website with D3, JQuery, and JavaScript
The live website is available at: http://borreliabase.org/~wgqiu/asm-challenge/