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Recommended analysis pipeline
We currently have a research analysis tool available in the Oxford Nanopore GitHub repository. The pipeline-umi-amplicon workflow is a proof of concept pipeline that creates consensus UMI reads from the raw FASTQ files. This tool is aimed at advanced users, and contains instructions for how to install and run the software.
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Overview of analysis
Figure 1. Bioinformatic analysis pipeline overview.Input
Input Type Description Basecalled 1D reads FASTQ Basecalled 1D reads Amplicon coordinates BED A BED file containing the regions on the reference genome that were targeted Reference genome FASTA Reference genome in FASTA format Output
Output Type Description Aligned UMI reads BAM Alignments of UMI reads Variant calls VCF Variant calls using varscan2 for UMI reads -
Example data
We have three different example data sets that demonstrate the implementation of the custom PCR UMI protocol from experimental design through to bioinformatic analysis.
Please refer to the Apps Update post Custom PCR UMI example data sets to view the in-depth data.