Top 61 Nextflow open source projects

Identification & characterization of bacterial plasmid-borne contigs from short-read draft assemblies.

Repository to host tool-specific module files for the Nextflow DSL2 community!

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

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

ARTIC SARS-CoV-2 workflow and reporting

A workflow for construction of Gene Expression count Matrices (GEMs). Useful for Differential Gene Expression (DGE) analysis and Gene Co-Expression Network (GCN) construction

No description, website, or topics provided.

Code to create a PRG from a Multiple Sequence Alignment file

GWAS Pipeline for H3Africa

Containerised components for cheminformatics and computational chemistry

TractoFlow: A robust, efficient and reproducible diffusion MRI pipeline leveraging Nextflow & Singularity

Rapid determination of appropriate reference genomes.

Workflows I find helpful for fungal genome annotation

NBIS/ELIXIR course: Tools for Reproducible Research

This repository has been archived, currently maintained version is at https://github.com/iii-companion/companion

(WIP) best-practices workflow for rare disease

Feature extraction algorithm for genomic data

An NGS read trimming tool that is specific, sensitive, and speedy. (production)

Bioinformatics pipeline for SARS-CoV-2 sequencing at CZ Biohub

NeoFlow: a proteogenomics pipeline for neoantigen discovery

Import a CWL workflow specification to Nextflow script (experimental)

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

Precision HLA typing from next-generation sequencing data

RNA-seq analysis pipeline for detection gene-fusions

VIRify: detection of phages and eukaryotic viruses from metagenomic and metatranscriptomic assemblies

A proof of concept of RNAseq pipeline

TOGA (Tool to infer Orthologs from Genome Alignments): implements a novel paradigm to infer orthologous genes. TOGA integrates gene annotation, inferring orthologs and classifying genes as intact or lost.

YAMP: Yet Another Metagenomic Pipeline

Example Nextflow pipelines and programming techniques

🔬 De novo assembly of nanopore reads using nextflow

Whole Exome/Whole Genome Sequencing alignment pipeline

A scalable bacterial genome assembly, annotation and analysis pipeline

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

Nanopore demultiplexing, QC and alignment pipeline

A simple RNA-Seq differential gene expression pipeline using Nextflow

A single-cell RNAseq pipeline for 10X genomics data

Nextflow basic tutorial for newbie users

SARS-CoV-2 workflow for nanopore sequence data

Computational workflows for metagenomics tasks, by the Bhatt lab

This repository contains the code necessary in order to reproduce the work contained in the submitted paper: "Segmentation of Nuclei in Histopathology Images by deep regression of the distance map".

A proof of concept RNA-Seq pipeline with Nextflow

RNA mapping pipeline

Our VM/Docker sharing infrastructure and management component

Multi-sample somatic variant caller

A pipeline for preprocessing NGS data from Illumina, Nanopore and PacBio technologies

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

A graphical user interface for distributed data processing of high throughput genomics

No description, website, or topics provided.

minimal example implementations for bioinformatics workflow managers

hybrid assembly and differential binning workflow for metagenomics, transcriptomics and pathway analysis