WtP: Phage identification via nextflow and docker or singularity

From QC to summary statistics

Nextflow pipeline encapsulating workflows for analyzing expansion lattice light-sheet microscopy (ExLLSM) imagery

A suite of bioinformatics data processing and analysis pipelines, software, and training resources for common methods.

Tools for processing HIC data.

A simple fastp-MultiQC nextflow pipeline

Nextflow workflows to assign Salmonella serotype based on Genome similarity using MASH, SOURMASH and KMA.

Automated virus amplicon sequencing analysis program integrated with Nextflow pipeline manager.

This is a demo about how to develop and deploy a pipeline using nextflow, scif, a container (Singularity and Docker) and its posterior deployment.

Filter a VCF to discard false positive variants

A nextflow pipeline for performing bacterial RNA-Seq data analysis.

Workflow for prOteome and tRanScriptome functiOnal aNnotation. CAUTION : project has moved to Gitlab.

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

This repo contains code that is relevant for the analysis (Mapping, BAM qc, Variant Calling, Filtering etc...) of IGSR data

cronology is an automated workflow for Cronobacter whole genome sequence assembly, subtyping and isolate clustering based on NCBI Pathogen Detection Project for Cronobacter.

RNA-Seq pipeline

Nextflow pipeline to assemble genomes from long reads.

EuroBioc2020 SPEAQeasy workshop https://eurobioc2020.bioconductor.org by Nick Eagles and Josh Stolz. For more information about SPEAQeasy check http://research.libd.org/SPEAQeasy/. For an example on how to use this RNA-seq processing pipeline and analyze the output files check http://research.libd.org/SPEAQeasy-example/.

A repository with usage examples of various pipeline and workflow orchestration tools

HLA typing pipelines in nextflow