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README.md
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__init__.py
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plot_kmer_cov.py
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run_QC_analysis.py
run_QC_analysis.py
 
 
run_QC_report.py
run_QC_report.py
 
 
run_assemblies.py
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run_assembly_report.py
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run_delivery.py
run_delivery.py
 
 
run_denovo.py
run_denovo.py
 
 
run_validation.py
run_validation.py
 
 

README.md

NGI specific scripts

scilifelab_denovo, automated convenience for NGI users.

Requirements

  • Fastq sequence data in the folder structure as delivered by NGI Stockholm
  • Needs to be run on UPPMAX.
  • Python packages reportlab and click

Installation

# Assuming NouGAT has been installed
source activate DeNovoPipeline
pip install reportlab click

The commandline tool scilifelab_denovo supports customizable parameter defaults for all it's sub-commands. It attempts to read a configuration file found in the file $HOME/.nougat/scilifelab.conf.

mkdir $HOME/.nougat
cp ../config_files/scilifelab.conf $HOME/.nougat/

# Now edit the template
vim $HOME/.nougat/scilifelab.conf