WtP: Phage identification via nextflow and docker or singularity

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

From QC to summary statistics

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

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

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

A simple fastp-MultiQC nextflow pipeline

Tools for processing HIC data.

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

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

A reproducible Nextflow DSL2 framework for standardized deployment, execution, and evaluation of single-cell foundation models (scFMs) with containerized environments and automated embedding inference.

Filter a VCF to discard false positive variants

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

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

nflaunch is a command-line tool to simplify launching Nextflow pipelines on cloud batch services (GCP Batch)

APEX: Automated Protein EXpression in E. coli

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

RNA-Seq pipeline

Nextflow pipeline to assemble genomes from long reads.

A Genome Annotation workflow for Eukaryotes