##Characterization of Prophages in Bacterial Genomes from the Honey Bee (Apis mellifera) Gut Microbiome
Raw sequences available at: Link Here
01_datacleaning: Cleaning of NCBI metadata of bacterial isolates and basic phage pipeline (merging phage datasets, confidence filtering, incorporating dereplication)
02_functionalcleaning: Merging functional analysis of phage (PHROGS & COG hits), identifying phage-associated proteins, estimating intactness.
03_descStats: Calculating min/median/max of number of prophage and prophage composition for total predicted and intact prophage. Table 1, Table S2 created here.
04_descGraphs: Fig1 and Fig2 made in ggplot, with relevant statistics present.
05_functanalysis: Functional analysis of phage proteins, Fig 3.
06_taxonomy: Classifying taxonomic families of phage, Fig 5. For code on how taxonomy was collected, see: https://github.com/scubalaina/phage_ref_ani_aai