GraftM is a pipeline used for identifying and classifying marker gene reads from metagenomic datasets
Project description
# GraftM
—
## Overview Basically, GraftM is a pipeline used for identifying and classifying marker gene reads from metagenomic datasets. If you are after a tool that provide rapid and accurate analysis of short read sequence data, then you’ll probably want to give GraftM a try
Head on over to the [GraftM page](http://geronimp.github.io/graftM/) for more general information.
Because GraftM is still being actively developed backwards incompatability may happen in the future, although we will aim to minimise this as much as possible.
—
## Installation The python code can be installed through pip: ` pip install graftm ` ### Dependencies GraftM requires a few extra binary applications as well, unfortunately: * orfm v. >= 0.2.0 (https://github.com/wwood/OrfM) * hmmer v. >= 3.1b1 (http://hmmer.janelia.org/) * fxtract (https://github.com/ctSkennerton/fxtract) * pplacer v. >= 2.6.32 (http://matsen.fhcrc.org/pplacer/) * krona v. >= 2.4 (http://sourceforge.net/p/krona/home/krona/)
—
## Help + Contact if you have any comments, complaints or reccomendations about GraftM. I’m happy to help, just ask through GitHub. A [manual](https://github.com/geronimp/graftM/wiki) is available in the form of the wiki here on github . Please just let us know if you think something might be useful to add to it.
Software by Joel A. Boyd and Ben J. Woodcroft Released under GPL3 - see LICENCE.txt for licencing details
—
Project details
Release history Release notifications | RSS feed
Download files
Download the file for your platform. If you're not sure which to choose, learn more about installing packages.