Home
Joel A. Boyd, Ben J. Woodcroft
GraftM is a tool for rapid, phylogenetically informed gene-centric analysis of sequence data. The main use of GraftM is as a meta-omic analysis pipeline that can rapidly generate community profiles by searching for and classifying gene families specified by the user. Basically, GraftM can be split into two phases. The first is the identification of reads of interest using Hidden Markov Models (HMMs), and the second phase is the placement of these reads into phylogenetic trees. The classification of sequences by GraftM is independent of traditional pairwise sequence comparison techniques, and provides a unique phylogenetic perspective to gene-centric community analysis. GraftM can be applied to:
- Metagenomes, metatranscriptomes, metaproteomes
- Assemblies, population, isolate or single cell genomes
- Amino acid or nucleic acid sequences
- Gzipped or uncompressed files
- FASTA or FASTQ formats
- GraftM is flexible. It accepts any type of sequence data in FASTA or FASTQ format.
- GraftM is user friendly. It provides a range of detailed run-time options so you can run GraftM they way you wish to.
- GraftM packages. GraftM runs with modular gene packages that can be annotated the way you like. GraftM packages allow you to customise the phylogenetic analysis of your data.
- Phylogenetically informed annotation. Provides a different perspective for community profiling, independent of pair-wise comparison techniques.
- GraftM packages - What are they? How are they created?
- Using GraftM - How do I use GraftM?
- Support - Questions? Bug reports? Tell us here.
GraftM relies on a number of non-python dependencies, all of which must be installed to run :
- OrfM v. >= 0.2.0
- HMMer v. >= 3.1b1
- fxtract
- pplacer v. >= 2.6.32
- Krona v. >= 2.4
- MAFFT v. >= 7.22
- DIAMOND v. >= 0.7.9
Stable versions of GraftM are available on pip:
pip install GraftM
If you find GraftM useful, please cite the git repository (https://github.com/geronimp/graftM)
GraftM is part of the M-tools suite. Please check out our other tools: