Welcome to the documentation of Master Of Pores 3

Master of Pores is a pipeline written in Nextflow DSL2 for the analysis of Nanopore data. It can handle reads from direct RNAseq, cDNAseq, DNAseq etc.

The pipeline is composed by four modules:

• mop_preprocess: preprocessing

• mop_mod: detecting chemical modifications. It reads the output directly from mop_preprocess

• mop_tail: estimating polyA tail size. It reads the output directly from mop_preprocess

• mop_consensus: it generates a consensus from the predictions from mop_mod. It reads the output directly from mop_mod

Contents:

• About Master of Pores 3
• Get Started
• MOP_PREPROCESS
• MOP_MOD
• MOP_CONSENSUS
• MOP_TAIL
• Resource reporting
• Benchmark
• CHANGELOG
• Continuous integration
• Troubleshooting