JHU Applied Physics Laboratory Biological Sciences

AGAVE

Automated Genomics Application for Variant Exploration (AGAVE)

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

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.

datasets

General repository for example datasets

mytax

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

mytax_marine

nCovIllumina

pathogenesis-gene-ontology

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

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.

TgIF

Trans-gene Insertion Finder

jhuapl-bio/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

jhuapl-bio/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.

jhuapl-bio/mytax

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

jhuapl-bio/AGAVE

Automated Genomics Application for Variant Exploration (AGAVE)

jhuapl-bio/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.

jhuapl-bio/pathogenesis-gene-ontology

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

jhuapl-bio/datasets

General repository for example datasets

jhuapl-bio/GE-Workshop-Sandbox

jhuapl-bio/mytax_marine

jhuapl-bio/nCovIllumina

jhuapl-bio/omics_workshop

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

jhuapl-bio/ONT-DART

jhuapl-bio/TgIF

Trans-gene Insertion Finder

jhuapl-bio/mytax_marine_old

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