CAMMiQ
github.com/algo-cancer/cammiqCAMMiQ is a software tool for microbial identification and quantification. Specifically, it builds a compact index to manage a database of microbial genomes (in particular, bacterial/viral genomes in NCBI RefSeq database) and answers queries of the following form: given a set of high throughput sequencing (HTS) reads obtained from a mixture of genomes in the database, identify the corresponding genomes (in the database) and compute their relative abundance.