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

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

A simple fastp-MultiQC nextflow pipeline

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

Tools for processing HIC data.

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

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.

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.

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

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/.

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

APEX: Automated Protein EXpression in E. coli