Pipeline to characterize and analyse fungal microbiomes

Installation & Getting started

• install nextflow

curl -s https://get.nextflow.io | bash

• pull the singularity image from the singularity hub

singularity pull shub://maxemil/Biodiversity-pipeline:master

• execute the pipeline with input.fasta, references.fasta (e.g. ) and information on the ecology of sequences

nextflow run maxemil/Biodiversity-pipeline --input_fasta input.fasta \
                      --reference_sequences references.fasta \
                      --environment_information ecology.tab \
                      --output_directory output \
                      -with-singularity maxemil-Biodiversity-pipeline-master.img

Dependencies

for the pipeline execution / container

• java >= 7
• nextflow (http://nextflow.io)
• singularity (recommended, http://singularity.lbl.gov/)

Tools

• MALT (http://ab.inf.uni-tuebingen.de/software/malt/)
• MEGAN6 (http://ab.inf.uni-tuebingen.de/software/megan6/)
• FUNGuild (https://github.com/UMNFuN/FUNGuild)
• vsearch (https://github.com/torognes/vsearch)
• spaced words (http://spaced.gobics.de/)
• python3
  • pandas
  • numpy
  • requests
• R
  • vegan
  • picante
  • VennDiagram

Testing

• To run an example analysis and check if the results are as expected, run

nextflow run maxemil/Biodiversity-pipeline --input_fasta test/input.fasta \
                      --reference_sequences test/references.fasta \
                      --environment_information test/ecology.tab \
                      --output_directory test/output \
                      -with-singularity maxemil-Biodiversity-pipeline-master.img