Nextflow Pipeline Modules (DSL2)

Nextflow pipeline modules and workflows for nanopore-driven bacterial genomics in DSL2

Consider to configure your network setup for distributed pipeline operation and resourcing with Netflow. Details for pipeline operations can be found in th corresponding repositories.

Pipelines

Purpose and modules of the main pipeline applications in np-core

:peacock: np-signal

nextflow run np-core/np-signal --help true

Signal level analysis pipeline for basecalling Fast5 files, and under development for NanoPath, Poremongo and Achilles linking into neural network training and adaptive sampling. Real-time basecalling and monitoring in the dashboard component Blobfish, the ugly deep sea cousin of MinKNOW.

• Guppy
• qcat

:drop_of_blood: np-pathogen

nextflow run np-core/np-pathogen --help true

Pipeline for detection and characteriziation of pathogens from metagenomic data, including real-time evaluation and reporting dashboard. Main component for the Queensland Genomics sepsis applications, DNA and RNA.

• nanoq
• checkm
• coverm
• fastp
• Kraken2
• Bracken
• Pathogen (links, regex, host removal, coverage)

:sauropod: np-phybeast

nextflow run np-core/np-phybeast --help true

Pipeline for phylogenomics and phylodynamics of bacterial pathogens using population-wide data, including subworkflows for outbreak attribution using nanopore data and Beastling implementation of bacterial Birth-Death model implementations on BEAGLE GPUs.

• Medaka
• Megalodon
• Snippy
• Gubbins
• Phybeast (date randomisation, variant sites)
• RAxML-NG
• TreeTime

:octopus: np-assembly

nextflow run np-core/np-assembly --help true

Pipeline for hybrid and nanopore bacterial genome assembly including final genotyping and annotations of the assemblies. I use the pipeline for both Illumina population genomics (genotyping from large collection of genome assemblies) and to process hybrid sequence data from multiplex bacterial runs.

• fastp
• rasusa
• dnadiff
• Flye
• Raven
• Shovill
• Racon
• Pilon
• Medaka
• Genotype (Mykrobe, Abricate, SCCion)