CoPTR: Compute Peak-to-Trough Ratio¶
The peak-to-trough ratio is the ratio of sequencing coverage near the replication origin to the replication terminus in a species of bacteria. PTRs are a valuable tool for investigating microbiome dynamics because they reflect a species’ replication rate at the time of sampling.
CoPTR is a tool for computing peak-to-trough ratios from metagenomic sequencing data from complete reference genomes and draft assemblies. CoPTR takes as input fastq files from multiple metagenomic samples and a reference database. It outputs the log2 PTR for each species in a sample.