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
Nextflow resequencing pipeline with bwa-mem and freebayes
Simple Nextflow RNA-Seq pipeline
a nextflow pacbiohifi for the genome assembly from the pacbiohifi. It also includes supports for the visualization and genome assessment.
Nextflow pipeline for Conpair (concordance and contamination estimator)
Nextflow wrapper for fastqc
Parallelization of Nextstrain builds and parameter testing using Nextflow
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