Flowchart for estimating AGS from a shotgun metagenome. 1) MicrobeCensus takes the first n reads of at least i base pairs from the shotgun metagenome and trims these reads down to i base pairs. 2) These reads are aligned against the database of essential genes using RAPsearch2. 3) A read is mapped to an essential gene family, j, if its top scoring alignment satisfies the mapping parameters, which are optimized for gene j and read length i. 4) Based on these mapped reads, the relative abundance of each essential gene family, R
j, is computed. 5) Next, we use R
to obtain an estimate of AGS for each gene. 6) Outlier predictions are removed and 7) MicrobeCensus takes a weighted average over the remaining estimates to produce a robust estimate of AGS for the shotgun metagenome. QC, quality control.