WITS Metagenomics Workshop

This repository provides model materials for the 2019 WITS metagenomics workshop in Johannesburg, SA.

Running the model workflow

1. Set up conda, singularity and nextflow, clone the Git repository

cd ~
mkdir -p ~/local/bin
export PATH="$PATH:~/local/bin"

wget -qO- https://get.nextflow.io | bash
wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh
bash Miniconda3*.sh #accept the defaults
conda install -c conda-forge singularity
git clone https://github.com/bhattlab/wits_workshop.git

Note: if singularity isn't supported on your compute cluster, set up environment manually instead.

conda install -y -c conda-forge -c bioconda -c r \
kraken2 krona kraken ncurses datrie r-ggplot2 r-doby r-rcolorbrewer r-scales r-plyr r-stringi
mkdir ~/miniconda/bin/taxonomy
ktUpdateTaxonomy.sh

git clone https://github.com/jenniferlu717/Bracken.git
cd Bracken
bash install_bracken.sh
cp bracken ~/local/bin/
cp bracken-build ~/local/bin/

2. Running the workflow

cd ~
mkdir test_run; cd test_run
~/nextflow ../wits_workshop/nextflow/taxonomic_classification/taxonomic_classification.nf  --tax_level S -resume -profile scg --in ../wits_workshop/nextflow/test_data/*.fq

Workflow Dependencies

Preprocessing

• fastqc
• trim-galore
• seqkit
• bwa
• samtools
  • prinseq
  • super-deduper
  • seqtk

Classification

• kraken2
  • krona (with databases)
  • bracken
• datrie
• r-ggplot2
• r-doby
• r-rcolorbrewer
• r-scales
• r-plyr

Assembly

• quast
• spades
• megahit

Strain comparisons

• bwa
• samtools
• bamtools
• bedtools
• MUSCLE
• FastTree
• r-ggplot2
• bioconductor-ggtree
• r-phangorn

Long read assembly

- python>3.5

• pilon
• bwa
• minimap2
• canu=1.7.1
• samtools
• bcftools
• bedtools #used with tombo
• bedops #used with tombo
• biopython
• pip
• tabix
• ncurses=6.1
• tensorflow #makes medaka work
• mummer
• circlator
• ONT albacore
  • quickmerge