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In addition, eResearch have developed a full 16S amplicon analysis pipeline using NextFlow. We recommend you use the bam files generated from this PacBio analysis as input for this pipeline:
16S amplicon analysis pipeline (NextFlow Ampliseq)
Running analysis on QUTs HPC
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If you haven’t been set up or have used the HPC previously, click on this link for information on how to get access to and use the HPC:
Need a link here for HPC access and usage
Creating a shared workspace on the HPC
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To request a node using PBS, submit a shell script containing your RAM/CPU/analysis time requirements and the code needed to run your analysis. For an overview of submitting a PBS job, see here:
Need a link here for creating PBS jobs
Alternatively, you can start up an ‘interactive’ node, using the following:
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module load bedtools bamToFastq#bamToFastq -i filename.sorted.bam -fq filename.sorted.fq for f1 in *.sorted.bam do echo working with $f1 bamToFastq -i $f1 -fq "${f1%%.sorted.bam}.fastq" done |
The fastq files can then be used in downstream analysis. Follow our ampliseq (16S analysis pipeline) guide here: