RNA sequencing analysis pipeline using STAR, RSEM, HISAT2 or Salmon with gene/isoform counts and extensive quality control.

Analysis pipeline to detect germline or somatic variants (pre-processing, variant calling and annotation) from WGS / targeted sequencing

A flexible pipeline for complete analysis of bacterial genomes

Amplicon sequencing analysis workflow using DADA2 and QIIME2

Eukaryotic Genome Annotation Pipeline-External caller scripts and documentation

Call and score variants from WGS/WES of rare disease patients.

Differential abundance analysis for feature/ observation matrices from platforms such as RNA-seq

(WIP) best-practices workflow for rare disease

A set of workflows written in Nextflow for Genome Annotation.

The Jackson Laboratory Data Science Nextflow based analysis workflows

A bioinformatics best-practice analysis pipeline for calling structural variants (SVs), copy number variants (CNVs) and repeat region expansions (RREs) from short DNA reads

TADA - Targeted Amplicon Diversity Analysis - a DADA2-focused Nextflow workflow for any targeted amplicon region

A nextflow pipeline for calling and annotating small germline variants from short DNA reads for WES and WGS data

Bact-Builder: Microbial de novo genome assembly pipeline

A nextflow pipeline for calling exome CNVs

Bacterial typing pipeline for clinical NGS data. Written in NextFlow, Python & Bash.

NYU Langone Genome PACT (Genome Profiling of Actionable Cancer Targets) targeted exome sequencing analysis pipeline.

WGS and WES data analysis pipeline

A bioinformatics pipeline that automates the Sanger amplicon sequencing data analysis of thousands of samples in parallel.

variant annotation workflow with VEP

Pipeline to assemble the genomes of eukaryotes.

Fastq preprocessor with optional contamination removal implemented in NextFlow. Supports short and long reads.