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decon

doc-annovar

Documentation for the ANNOVAR software

fastp

An ultra-fast all-in-one FASTQ preprocessor (QC/adapters/trimming/filtering/splitting/merging...)

gatk4-somatic-snvs-indels

This repo has been archived, these workflows are still available in the GATK repository under the scripts directory. The workflows are also organized in Dockstore in the GATK Best Practices Workflows collection.

gemini

a lightweight db framework for exploring genetic variation.

mavis

Merging, Annotation, Validation, and Illustration of Structural variants

migmap

HTS-compatible wrapper for IgBlast V-(D)-J mapping tool

ontdecipher

deCIPHER is a pipeline for amplicon-based Oxford Nanopore Technology (ONT) sequencing to analyze and assess SARS-CoV-2 and other pathogens genetic diversity.

parliament2

Runs a combination of tools to generate structural variant calls on whole-genome sequencing data

spectre

A computational toolkit in R for the integration, exploration, and analysis of high-dimensional single-cell cytometry and imaging data.

spliceai

A deep learning-based tool to identify splice variants