This is a Docker clone of the popular UCSC web browser, currently used primarily for analyzing malaria genomic data. The page includes a public site (for disseminating published study results) and a private site (for viewing unpublished data). Charlie Simkin (my brother and business partner at Simkin Bioinformatics LLC) created the docker files for this and figured out how to host password protected sites. Charlie also created a snakemake pipeline for creating annotation hubs. I populated the site with an annotated 3D7 malaria strain and with MIP and amplicon panels. I also developed a snakemake pipeline for mapping amplicon panels (and MIPs) to UCSC genome browser track hubs and Charlie and I co-developed a pipeline for converting mapped bam reads to bam and bigwig track hubs
MIPtools visualizations:
Mapping transposable elements to genomes:
Alfred Simkin 