JHU Applied Physics Laboratory Biological Sciences

Basestack

Basestack is a platform for rapid and real time analysis of NGS data. It provides a executable application that connects standard bionformatics tools to a user interface. It is usable on all major Linux distributions, Mac OS, and Windows 10 or later

taxtriage

TaxTriage is a Nextflow workflow designed to agnostically identify and classify microbial organisms within short- or long-read metagenomic NGS data. This flexible tool was developed with various use-cases of mNGS in mind.

mytax

mytax is a tool for building custom taxonomies, useful for nucleotide sequence classification

AGAVE

Automated Genomics Application for Variant Exploration (AGAVE)

basestack_consensus

This repository is a Dockerized pipeline for creating consensus viral genomes from Oxford Nanopore data. This pipeline leverages the ARTIC Network bioinformatics pipeline and couples many annotation and reporting tools, resulting in an automatically generated PDF report. The pipeline is built to be deployed in the Basestack platform (https://github.com/jhuapl-bio/Basestack) so that anyone, regardless of bioinformatics expertise, can run it and make use of its automated consensus genomes and reports.

pathogenesis-gene-ontology

An ontology for the functional annotation of genes and gene products involved in pathogenesis

datasets

General repository for example datasets

GE-Workshop-Sandbox

mytax_marine

nCovIllumina

ONT-DART

TgIF

Trans-gene Insertion Finder

mytax_marine_old

mytax with added information on marine organisms, including common names, pictures, and population distribution

omics_workshop

This is the central repository for data and example commands for bioinformatics workshop used for JHU-APL faculty and participant use