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README.md
iMGMC-16SrRNA-alignment.fasta
iMGMC-CopyNr-16SrRNA.tab
iMGMC-KO_traits.tab
iMGMC-MAGs16SrRNAlinks.tab
iMGMC-PICRUSt.bash
picrust-workflow-default.png
picrust-workflow-denovo.png

README.md

iMGCM - Mouse gut specific PICRUSt workflow

Table of Contents

Description
Requirements
Workflow

Description

PICRUSt with iMGMC data

  • data form diverse mouse samples from different studies (12 Vendors incl. wild mice and various gut locations)
  • using MAGS to 16S rRNA gene linkage

Requirements

  • PICRUSt 1.1.3
  • pynast
  • FastTree
  • iMGMC repository (/PICRUst/iMGMC-PICRUSt.bash)

Bioconda

Please use Conda to install needed enviroment over the Bioconda channel:

conda create iMGMC-PICRUSt -c bioconda picrust pynast fasttree

Workflow

picrust-workflow-denovo

Needed input files

  • BiomFile, your abundance table in biom format
  • OTUseq, your OTU sequences in fasta format

Pipeline

Quick start:

conda activate iMGMC-PICRUSt
iMGMC-PICRUSt.bash BiomFile.biom OTUseq.fasta

Please cite our paper:

An integrated metagenome catalog enables novel insights into the murine gut microbiome
Till R. Lesker, Abilash C. Durairaj, Eric. J.C. Gálvez, John Baines, Thomas Clavel, Alexander Sczyrba, Alice C. McHardy, Till Strowig http://biorxiv.org/cgi/content/short/528737v1

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