Scripts used in microbiome analysis in Schizaphis graminum

These scripts were used to download reference and representative microbial genomes from NCBI, attribute RNAseq counts to a closest hit among multiple sam files from bwa mem runs, and aggregate RNAseq counts by hit taxon at various levels in a taxonomic hierarchy.  They were used in a general strategy to count organisms based on unamplified transcripts mapped in parallel to tens of thousands of whole genomes.  A manuscript has been submitted to Insect Molecular Biology to report the results of this study.