A PluMA pipeline that runs the MiSeq SOP metagenomics example from the Mothur tutorial, followed by some downstream analysis.
Switch branches/tags
Nothing to show
Clone or download
Fetching latest commit…
Cannot retrieve the latest commit at this time.
Permalink
Type Name Latest commit message Commit time
Failed to load latest commit information.
output
F3D0_S188_L001_R1_001.fastq
F3D0_S188_L001_R2_001.fastq
F3D141_S207_L001_R1_001.fastq
F3D141_S207_L001_R2_001.fastq
F3D142_S208_L001_R1_001.fastq
F3D142_S208_L001_R2_001.fastq
F3D143_S209_L001_R1_001.fastq
F3D143_S209_L001_R2_001.fastq
F3D144_S210_L001_R1_001.fastq
F3D144_S210_L001_R2_001.fastq
F3D145_S211_L001_R1_001.fastq
F3D145_S211_L001_R2_001.fastq
F3D146_S212_L001_R1_001.fastq
F3D146_S212_L001_R2_001.fastq
F3D147_S213_L001_R1_001.fastq
F3D147_S213_L001_R2_001.fastq
F3D148_S214_L001_R1_001.fastq
F3D148_S214_L001_R2_001.fastq
F3D149_S215_L001_R1_001.fastq
F3D149_S215_L001_R2_001.fastq
F3D150_S216_L001_R1_001.fastq
F3D150_S216_L001_R2_001.fastq
F3D1_S189_L001_R1_001.fastq
F3D1_S189_L001_R2_001.fastq
F3D2_S190_L001_R1_001.fastq
F3D2_S190_L001_R2_001.fastq
F3D3_S191_L001_R1_001.fastq
F3D3_S191_L001_R2_001.fastq
F3D5_S193_L001_R1_001.fastq
F3D5_S193_L001_R2_001.fastq
F3D6_S194_L001_R1_001.fastq
F3D6_S194_L001_R2_001.fastq
F3D7_S195_L001_R1_001.fastq
F3D7_S195_L001_R2_001.fastq
F3D8_S196_L001_R1_001.fastq
F3D8_S196_L001_R2_001.fastq
F3D9_S197_L001_R1_001.fastq
F3D9_S197_L001_R2_001.fastq
Mock_S280_L001_R1_001.fastq
Mock_S280_L001_R2_001.fastq
README.md
config.Mouse.txt
getPlugins.sh
input.mothur
network.gml
network.visualization.txt
silva.bacteria.fasta.zip
stability.files
trainset9_032012.pds.fasta
trainset9_032012.pds.tax

README.md

Mouse

A PluMA pipeline that runs the MiSeq SOP metagenomics example from the Mothur tutorial, followed by some downstream analysis.

Mothur Tutorial is available at: https://www.mothur.org/wiki/MiSeq_SOP Results of their experiment were published in:

Kozich JJ, Westcott SL, Baxter NT, Highlander SK, Schloss PD. (2013): Development of a dual-index sequencing strategy and curation pipeline for analyzing amplicon sequence data on the MiSeq Illumina sequencing platform. Applied and Environmental Microbiology. 79(17):5112-20.

To run this pipeline:

  1. Clone this repository into the pipelines/ directory of PluMA.
  2. Change to the new Mouse/ subdirectory.
  3. Run ./getPlugins.sh to automatically download all relevant PluMA plugins.
  4. Change to the PluMA root directory: 'cd ../../'
  5. Install the (currently) latest versions of Mothur (1.39.5, mothur.org), Cytoscape (3.6.0, cytoscape.org) and SCons (3.0.1, scons.org) and be sure they are in your system PATH.
  6. Run 'scons perl=0'
  7. Run './pluma pipelines/Mouse/config.Mouse.txt'