1 Tools, Resources, and Environments

1.1 Essential Read QC tools

• Seqkit
• Fastqc
• MultiQC
• BBDuk script
• Trimmomatic
• Kneaddata

1.2 Required QC resources

• Adapter fasta files
• PhiX fasta file

1.3 Basic YAML file for read QC (environment.yml)

name: readqc
channels:
    - bioconda
    - biobakery
dependencies:
    - seqkit =2.3.1
    - fastqc =0.12.1
    - multiqc =1.14
    - bbmap =39.01
    - trimmomatic =0.39
    - knead-data =0.12.0

1.4 Creating an environment for QC

conda activate base
mamba install -c bioconda -c biobakery -c conda-forge -n readqc -file environment.yml