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The Knutt Pipeline

Snakefiles for the paper

This pages describes how to accquire the pipelines used in the workflow. All pipelines require conda and Snakemake.

conda create -y -n snake -c bioconda -c conda-forge snakemake>=5.10 sra-tools
conda activate snake

KnuttReads2Bins

Read analysis and binning.

git clone -b paper https://github.com/KnuttPipeline/KnuttReads2Bins.git
cd KnuttReads2Bins
download_sra(){
  fastq-dump --split-files -O input $1 --gzip
  mv input/${1}_1.fastq.gz input/${2}_R1.fastq.gz
  mv input/${1}_2.fastq.gz input/${2}_R2.fastq.gz
}
download_sra SRR11128853 ENR-Ac244days_meta
download_sra SRR11128854 ENR-Ac211days_meta
download_sra SRR11128855 PFL9_meta
snakemake -prj 16 --use-conda --keep-going paper 2>&1 | tee run.log
# Run with 16 cores available

KnuttBinAnno

Bin annotation.

git clone -b paper https://github.com/KnuttPipeline/KnuttBinAnno.git
cd KnuttBinAnno
wget -qO- https://www.knutt.org/assets/etc/binsdyksma.tgz | tar xzvf - -C input/
snakemake -prj 16 --use-conda --keep-going paper 2>&1 | tee run.log

KnuttBinPhylo

Automatic phylognetic marker analysis.

git clone -b paper https://github.com/KnuttPipeline/KnuttBinPhylo.git
cd KnuttBinPhylo
wget -qO- https://www.knutt.org/assets/etc/binsdyksma.tgz | tar xzvf - -C input/
snakemake -prj 16 --use-conda --keep-going paper 2>&1 | tee run.log