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an-introduction-to-applied-bioinformatics

Interactive lessons in bioinformatics.

artic-measles

Repository for realtime sequencing of measles virus using the MinION

artic-ncov2019

ARTIC nanopore protocol for nCoV2019 novel coronavirus

artic-rsv

augur

Pipeline components for real-time phylodynamic analysis

b117-rt-qpcr-design

Basic commands and scripts used to identify sars2 B117 lineage-specific and B1351 lieanege-specific genomic signatures

basecalling-comparison

A comparison of different Oxford Nanopore basecallers

basestack

Basestack is a platform for rapid and real time analysis of Nanopore generated sequencing data. Basestack comes bundled with a series of both cutting edge public tools, some modified by JHU built phylogenetic and genomic pipelines, all integrated into a user interface ( that is quickly and seamlessly installable on all standard laptops on any of the major operating systems used today. Ultimately, the suite provides users with a means of quickly and accurately generating consensus sequences from viral data within minutes of starting. In addition, we provide a system for automated updates once the application is installed for any future changes or additions to the application.

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.

bayesian-stats-with-r

Material for a workshop on Bayesian stats with R

bear

BEAR: viral diagnostic analysis pipeline for SARS-CoV-2

bioinfo-combio

The rendered book can be found at https://liulab-dfci.github.io/bioinfo-combio/

bioinformatics-books

"Every single cell in the human body replaces itself over a period of seven years. That means there's not even the smallest part of you now that was part of you seven years ago." ― Steven Hall

bionumpy

Python library for array programming on biological datasets. Documentation available at: https://bionumpy.github.io/bionumpy/

biopython.github.io

Source of biopython.org website, migrated from MediaWiki

cecret

Nextflow workflow for our analysis of SARS-COV-2

clairs

ClairS - a deep-learning method for long-read somatic small variant calling

computer-science

:mortar_board: Path to a free self-taught education in Computer Science!

constellations

covariants

Real-time updates and information about key SARS-CoV-2 variants, plus the scripts that generate this information.

datacarpentry.github.io

Data Carpentry website

ecdc_virology

Public virology code from ECDC bioinformatics

epi2me-api

API for communicating with the EPI2ME Platform for nanopore data analysis. Used by EPI2ME Agent & CLI.

flye

De novo assembler for single molecule sequencing reads using repeat graphs

gatk

Official code repository for GATK versions 4 and up

gb2seq

Use a GenBank file to extract sequences for features and other information from another genome

grinch

global report investigating novel coronavirus haplotypes

hatchet

HATCHet (Holistic Allele-specific Tumor Copy-number Heterogeneity) is an algorithm that infers allele and clone-specific CNAs and WGDs jointly across multiple tumor samples from the same patient, and that leverages the relationships between clones in these samples.

hecatomb

hecatomb is a virome analysis pipeline for analysis of Illumina sequence data

influenza_r9.4.1_rbk_2022

In-house python scripts for influenza virus sequencing using Nanopore, made available to accompany https://doi.org/MGEN-D-23-00116