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
Simple Nextflow RNA-Seq pipeline
Nextflow resequencing pipeline with bwa-mem and freebayes
Nextflow pipeline for Conpair (concordance and contamination estimator)
Nextflow wrapper for fastqc
Parallelization of Nextstrain builds and parameter testing using Nextflow
Bacterial phenotype prediction from low pass sequencing using recommender systems and machine learning classifiers.
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