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nanoplot, porechop_abi, chopper, seqkit |
For example, search for nanoplot:
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conda install bioconda::chopper |
Finally, let’s install the seqkit suite of tools:
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conda install bioconda::seqkit |
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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