Nextflow pipeline for analysis of direct RNA Nanopore reads

A collection of unexpected challenges and learnings with nextflow and nf-core.

A proof of concept daisy-chaining Nextflow workflows

NeoFlow: a proteogenomics pipeline for neoantigen discovery

TransPi – a comprehensive TRanscriptome ANalysiS PIpeline for de novo transcriptome assembly

A bioinformatics best-practice analysis pipeline for calling structural variants (SVs), copy number variants (CNVs) and repeat region expansions (RREs) from short DNA reads

A pipeline for comprehensive genomic analyses of Mycobacterium tuberculosis with a focus on clinical decision making as well as research

Nextflow pipeline for genome annotation of protein-coding genes

Workflow for MAG quality assessment and taxonomical annotation.

A bioinformatics best-practice analysis pipeline for the analysis of shallow whole genome sequencing (sWGS) data for the identification of copy number alterations (CNAs).

Sanger Cellular Genetics single-cell ATAC-seq pipeline.

avantonder/assembleBAC-ONT is a bioinformatics pipeline that de novo assembles and annotates Oxford Nanopore (ONT) long-read sequence data.

Flujos de trabajos desarrollados y automatizados en el Intituto Nacional de Medicina Genómica para el procesamiento de datos genómicos y transcriptómicos.

Bacterial Assembly and Antimicrobial Resistance Genes In NextFlow

Nextflow workflow for performing DIA proteomics

bacQC is a bioinformatics analysis pipeline for assessing the quality of bacterial isolate sequence data

Template for creating Nextflow DSL2 pipelines

A Nextflow pipeline demonstrating how to train graph neural networks for gene regulatory network reconstruction using DREAM5 data.

A Nextflow pipeline for end-to-end long-read proteogenomics analysis