Virus reassortment inference software. Infers both recent and ancestral reassortment and uses flexible molecular clock constraints.

Nextstrain build for SARS-CoV-2

Structured metadata for your FASTA sequences.

A mode to facilitate interactive data visualization using Vega from within emacs

PyMC educational resources

Quickly search, compare, and analyze genomic and metagenomic data sets.

💻 command-line bootcamp adventure in your browser

viral-ngs: command line tools and wrappers for processing raw viral genomic data

A simple way to use GitHub OAuth to serve a protected Jekyll site to your GitHub organization

An imagemagick-like frontend to Biopython SeqIO

Convert SAM format to PSL format

aka "Bayesian Methods for Hackers": An introduction to Bayesian methods + probabilistic programming with a computation/understanding-first, mathematics-second point of view. All in pure Python ;)

A tool set for short variant discovery in genetic sequence data.

Validated, scalable, community developed variant calling, RNA-seq and small RNA analysis

GATK QScripts used in our illumina variant calling pipeline.

Structural variant detection and association testing

Map sequence from Molecular Inversion Probes with BWA, strip arms, de-dup, ..., profit

GenomeTools genome analysis system.

C++ API & command-line toolkit for working with BAM data

Web based LIMS

BioRepo is a LIMS for HTS data @ EPFL - Vital-IT

A standalone and lightweight C library

cython wrapper to fastahack

Tools for next-generation sequencing analysis

Django admin interface for validating and saving uploaded CSV files as form data.

Arbitrary CSV data importer for Django

Official code repository for GATK versions 1.0 through 3.7 (core engine). For GATK 4 code, see the https://github.com/broadinstitute/gatk repository