Assembly and binning of metagenomes

Nanopore demultiplexing, QC and alignment pipeline

Highly parallelised multi-taxonomic profiling of shotgun short- and long-read metagenomic data

Assembly and intrahost/low-frequency variant calling for viral samples

Simple bacterial assembly and annotation pipeline

Multi-platform genome assembly pipeline for Illumina, Nanopore and PacBio reads

SARS-CoV-2 workflow for nanopore sequence data

A Nextflow workflow for QC, evaluation, and profiling of metagenomic samples using short- and long-read technologies

A Nextflow full-length 16S profiling pipeline for ONT reads

Master of Pores 2

Single-cell/nuclei pipeline for data derived from Oxford Nanopore and 10X Genomics

🔬 De novo assembly of nanopore reads using nextflow

An analysis pipeline for long-reads from both PacBio and Oxford Nanopore Technologies (ONT), written in Nextflow.

Basic workflow for nanopore sequencing data

A pipeline to identify (and remove) certain sequences from raw genomic data. Default taxon to identify (and remove) is Homo sapiens. Removal is optional.

UNDER CONSTRUCTION: Hybrid genome assembly pipeline using a combination of long and short sequencing reads

Pipeline for hybrid assembly using short and long reads.

Comprehensive pipeline for detection of TB from ONT adaptive sequencing and amplicon data.

Nextflow pipeline to assemble genomes from long reads.

Pathogen whole genome sequence (WGS) data analysis pipeline