# Using Hi-C to link bacterial host genomes to mobile elements and antimicrobial resistance genes. This repo contains the code (and some of the data) to do the basic analyses in our paper. ## Data Raw sequencing data and de novo assemblies are available from NCBI Sequence Read Archive via BioProject accession PRJNA506462. Processed data are in the `data/` directory of this repo. `WW_mags.tar.gz` is an archive of the untreated wastewater (WW) ProxiMeta clusters, whereas `WWEC_mags.tar.gz` contains the ProxiMeta clusters from the wastewater+E. coli spike-in sample. These genome clusters are similar to what some call "bins" or "metagenome-assembled genomes (MAGs)". We also include abundance estimates from kallisto for contigs of both de novo assemblies. Last, we provide Hi-C contact information about the contigs in the two assemblies in the form of the `WW_links.counts.gz` and `WWEC_links.counts.gz` files, and lists of the mobile element contigs of interest. ## Analyses See the `code/` directory for scripts used in this project. For more information about how these scripts were used please see the ["Data analysis methods"][1] wiki page. [1]: https://osf.io/ezb8j/wiki/Data%20analysis%20methods/