A Custom Variant Calling Pipeline for Dengue WGS (BWA + GATK + Lofreq) using nextflow and docker
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Updated
Dec 9, 2017
A Custom Variant Calling Pipeline for Dengue WGS (BWA + GATK + Lofreq) using nextflow and docker
This is a demo about how to develop and deploy a pipeline using nextflow, scif, a container (Singularity and Docker) and its posterior deployment.
A directory structure to build a workspace for experiments.
Proof of concept of a RNA-Seq pipeline from reads to count matrix (including quality control) with Nextflow and additional example RNA-Seq analysis in R
Nextflow Scripts/Workflows for Bioinformatics
Variant calling nextflow pipeline for Grapedia " Tinkering with GRAPEDIA Training School: a modern take on grapevine data analysis" (DATE: 26-28 June 2023 VENUE: FEM | Fondazione Edmund Mach, Via E. Mach 1, 38098 San Michele all’Adige, Trento, Italy)
Simple Nextflow RNA-Seq pipeline
Nextflow resequencing pipeline with bwa-mem and freebayes
Nextflow wrapper for fastqc
Nextflow wrapper for snippy
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