Skip to main content

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 incompatibility 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 A [manual](https://github.com/geronimp/graftM/wiki) is available in the form of the wiki here on github.

If you have any further comments, complaints or recomendations about GraftM, drop an email to the [SupportM](https://groups.google.com/forum/?hl=en#!forum/supportm) public help forum.

— Software by Joel A. Boyd (http://ecogenomic.org/users/joel-boyd) (@geronimp) and [Ben J. Woodcroft](http://www.ecogenomic.org/users/ben-woodcroft) (@wwood) at the [Australian Centre for Ecogenomics](http://ecogenomic.org) Released under GPL3 - see LICENCE.txt for licencing details

Project details


Download files

Download the file for your platform. If you're not sure which to choose, learn more about installing packages.

Source Distribution

graftm-0.5.2.tar.gz (48.7 kB view hashes)

Uploaded Source

Supported by

AWS AWS Cloud computing and Security Sponsor Datadog Datadog Monitoring Fastly Fastly CDN Google Google Download Analytics Microsoft Microsoft PSF Sponsor Pingdom Pingdom Monitoring Sentry Sentry Error logging StatusPage StatusPage Status page