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microbecensus website  

MicrobeCensus is a fast and easy to use pipeline for estimating the average genome size (AGS) of a microbial community from metagenomic data.

In short, AGS is estimated by aligning reads to a set of universal single-copy gene families present in nearly all cellular microbes (Bacteria, Archaea, Fungi). Because these genes occur once per genome, the average genome size of a microbial community is inversely proportional to the fraction of reads which hit these genes.

Once AGS is obtained, it becomes possible to obtain the total coverage of microbial genomes present in a sample (genome equivalents = total bp sequenced/AGS in bp), which can be useful for normalizing gene abundances.

Required Modules


  • gcc/5.2.0
  • microbecensus

System Variables

  • HPC_MICROBECENSUS_DIR - installation directory


If you publish research that uses microbecensus you have to cite it as follows:

Nayfach, S. and Pollard, K.S. Average genome size estimation improves comparative metagenomics and sheds light on the functional ecology of the human microbiome. Genome biology 2015;16(1):51.