RNA sequencing analysis pipeline using STAR, RSEM, HISAT2 or Salmon with gene/isoform counts and extensive quality control.

Analysis pipeline to detect germline or somatic variants (pre-processing, variant calling and annotation) from WGS / targeted sequencing

A flexible pipeline for complete analysis of bacterial genomes

Assembly and binning of metagenomes

Nanopore demultiplexing, QC and alignment pipeline

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

Eukaryotic Genome Annotation Pipeline-External caller scripts and documentation

NanoCLUST is an analysis pipeline for UMAP-based classification of amplicon-based full-length 16S rRNA nanopore reads

Nextflow pipeline for analysis of direct RNA Nanopore reads

WtP: Phage identification via nextflow and docker or singularity

Generic but comprehensive pipeline for prokaryotic genome annotation and interrogation with interactive reports and shiny app.

(Meta-)genome screening for functional and natural product gene sequences

A Nextflow pipeline for running the ARTIC network's fieldbioinformatics tools (https://github.com/artic-network/fieldbioinformatics), with a focus on ncov2019

Nextflow pipeline to analyze PacBio HiFi full-length 16S data

nextNEOpi: a comprehensive pipeline for computational neoantigen prediction

MycoSNP: Whole Genome Sequencing Analysis of Fungal Isolates

Precision HLA typing from next-generation sequencing data

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

A mapping-based pipeline for creating a phylogeny from bacterial whole genome sequences

Reference-based consensus creation

ARTIC SARS-CoV-2 workflow and reporting

AMR++ is a bioinformatic pipeline meant to aid in the analysis of raw sequencing reads to characterize the profile of antimicrobial resistance genes, or resistome.

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

Metagenomic Estimation of Dietary Intake and Content.

A pipeline for bioinformatics analysis of bacterial genomes

Bacterial surveillance pipeline.

Influenza genome analysis Nextflow workflow

Short idioms and patterns for transforming, merging and managing files and channels in Nextflow.