README.md

PipeRline

PipeRline is a targets based Metabarcoding pipeline implemented in R

The best place to start is going through the General introduction to the pipeRline workflow

Note that this pipeline is primarily intended for internal use at Agriculture Victoria, and may change regularly with no notice. Use at your own risk.

Project specific workflows:

Workflows for local PC:

• Insect COI

• Tephritid surveillance (COI + EIF3L)

• Marine surveillance (COI + 18S)

• Bee health (16S + ITS)

Workflows for BASC HPC:

• Insect COI on BASC HPC server

• Marine surveillance (COI only) on BASC HPC server

Experimental:

• Insect COI with UMIs