My final thesis project work from my Biomedical Genomics MSc undertaken at NUIG, 2021. Includes Nextflow, Snakemake, Bash, Python and R scripts.
Working through NextFlow tutorials. See https://github.com/nextflow-io/training
Next-generation Sequencing workflows
This directory contains material that I've used in different courses
Bayesian phylogenetic analysis
A simple pipeline to test some basic nextflow features.
A nextflow pipeline for analysis and visualisation of NGS data using FastQC and Python Ploty Dash.
Nextflow pipeline to assemble genomes from long reads.
A nextflow workflow to build referenceseeker DBs on the fly
Nextflow pipeline for targeted sequencing data.
A Nextflow pipeline for performing bacterial RNA-Seq analysis without a reference genome.
Filter a VCF to discard false positive variants
An hello world pipeline to test nextflow installations.
Testing different pipelines using Nextflow
nflaunch is a command-line tool to simplify launching Nextflow pipelines on cloud batch services (GCP Batch)
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/.
Nextflow Scripts/Workflows for Bioinformatics
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