GraftM is a meta-omic tool that identifies and classifies marker genes in short read datasets (metagenomes and metatranscriptomes), as well as assembled contigs, whole genomes and protein sequences. GraftM outputs a taxonomic/functional summary table, a krona plot, as well as various other run statistics. Both unaligned and aligned "hit" sequences are provided.

GraftM is designed for speed and accuracy. It is able to find marker genes in a 200Mb of assembled metagenome in <20 sec, and compares favourably with similar tools in accuracy benchmarking.

News + Updates

31/03/2015 - Please submit any requests for features in GraftM to the GitHub page!

Getting GraftM

GraftM has a few dependencies, which are needed to use all the features of GraftM. The manual has more detailed instructions on how to install GraftM, its dependencies, and a description of command line options.

The source code for GraftM is also available on GitHub.


Written by Joel Boyd, Ben Woodcroft and Gene Tyson, GraftM is licensed using the Lesser GNU General Public License version 3 as published by the Free Software Foundation.

Using GraftM

GraftM was developed as a tool for the rapid analysis of short read metagenomic data. It was developed as a tool that could search and classify marker gene reads, without using pairwise sequence comparisons such as BLAST. The result is a flexible, easy-to-use tool that can be run on any gene: all in a fraction of the time required by other methods.

We provide some GraftM packages, such as 16S rRNA, mcrA and pmoA, but for detailed instructions on how to create your own GraftM package, please visit the manual page.

Example Usage

Here is just a quick example of how to run GraftM. You can find some example data to use GraftM with here.

$ graftM graft --forward reads_f.fa --graftm_package mcrA_gpkg

Citing GraftM

If you use GraftM then please cite us. As of yet we have no publication, but please cite the GitHub page.


Of course, you can always contact Joel or Ben on the issues page for any issues that you encounter with GraftM. Alternatively you could just send us an email through supportm@googlegroups.com. We're more than happy to help.

The M suite

GraftM is part of the M(etagenomics) suite of tools being developed at the Australian Centre for Ecogenomics (ACE). We'd love for you to check out our tools:

  • GroopM - Recover (bin) population genomes from assembled metagenomes using differential coverage across multiple datasets.
  • CheckM - Assess the quality of genomes recovered from isolates, single cells or metagenomes using lineage specific marker sets.
  • BamM - Make and parse metagenomic BAM files.

This website's structure and the GraftM logo are copyright Mike Imelfort. This site was created using a template created by the wonderful people at bootswatch.