Stage 1 pipeline

svAmplicon data analysis first entails execution of a pipeline with primary actions:

• align = align input fastq files to the reference genome
• extract = scan aligned reads to identify amplicon boundaries and nominate unique reads with structural variants (SVs)

Pipeline inputs

The primary inputs to the svAmplicon pipeline are:

• genome files as described under Installation
• two FASTQ format read files per sample, obtained from a paired-end, short-read sequencing platform.

Pipeline outputs

The svAmplicon pipeline produces alignment bam files and an app data package for interactive visualization, *.mdi.package.zip.

Pipeline options

Options for the different pipeline actions can be listed as follows:

mdi svAmplicon <action> --help

Pipeline job files

The best way to configure pipeline execution is using YAML job files. The source publication provides comlete examples for the reported samples.