skip to navigation
skip to content

Not Logged In

GroopM 0.2.10

Metagenomic binning suite

Latest Version:

.          .d8888b.                                    888b     d888
.         d88P  Y88b                                   8888b   d8888
.         888    888                                   88888b.d88888
.         888        888d888 .d88b.   .d88b.  88888b.  888Y88888P888
.         888  88888 888P"  d88""88b d88""88b 888 "88b 888 Y888P 888
.         888    888 888    888  888 888  888 888  888 888  Y8P  888
.         Y88b  d88P 888    Y88..88P Y88..88P 888 d88P 888   "   888
.          "Y8888P88 888     "Y88P"   "Y88P"  88888P"  888       888
.                                             888
.                                             888
.                                             888


GroopM is a metagenomic binning toolset. It leverages spatio-temoral
dynamics to accurately (and almost automatically) extract genomes
from multi-sample metagenomic datasets.

GroopM is largely parameter-free. Use: groopm -h for more info.

See also:


Should be as simple as

    pip install GroopM

Data preparation and running GroopM

Before running GroopM you need to prep your data. A typical workflow looks like this:

    1. Produce NGS data for your environment across mutiple (3+) samples (spearated spatially or temporally or both).
    2. Co-assemble your reads using Velvet or similar.
    3. For each sample, map the reads against the co-assembly. GroopM needs sorted indexed bam files. If you have 3 samples then you will produce 3 bam files. I use BWA / Samtools for this.
    4. Take your co-assembled contigs and bam files and load them into GroopM using 'groopm parse' saveName contigs.fa bam1.bam bam2.bam...
    5. Keep following the GroopM workflow. See: groopm -h for more info.

Licence and referencing

Project home page, info on the source tree, documentation, issues and how to contribute, see

This software is currently unpublished but a manuscript is being prepared. Please contact me at m_dot_imelfort_at_uq_dot_edu_dot_au for more information about referencing this software.

Copyright © 2012 Michael Imelfort. See LICENSE.txt for further details.
File Type Py Version Uploaded on Size
GroopM-0.2.10.tar.gz (md5) Source 2013-07-26 119KB
  • Downloads (All Versions):
  • 5 downloads in the last day
  • 468 downloads in the last week
  • 2412 downloads in the last month