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Create working folder and copy data

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conda install bioconda::seqkit

Alternative approach to create a conda env and install tools (we are not doing this - this just for your information) - installing all tools at once (slower option!)

Prepare the following environment.yml file:

name: ONTvariants_QC
channels:
  - conda-forge
  - defaults
  - bioconda
dependencies:
  - nanoplot=1.42.0
  - porecho=0.2.4
  - porechop_abi=0.5.0
  - chopper=0.8.0

Create a new environment:

conda env create -f environment.yml

Running QC

Now that we have installed all the tools needed for the QC of Nanopore reads, let’s run the preprocessing of reads.

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As outputs find the porechop_abi processed file (SRR17138639_1_porechop_abi.fastq) and the chopper output (SRR17138639_1_porechop_abi_chopper_q10_300b.fastq). To visualise the QC reports, let’s connect to the HPC via file finder (see below).

NOTE: To proceed, you need to be on QUT’s WiFi network or signed via VPN.

To browse the working folder in the HPC type in the file finder:

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