BLAST comparison with faster programs, like BLAST, BLAST fast, Diamond, Usearch (local and ublast), Mmseq2.

A basecaller for Oxford Nanopore Technologies' sequencers

Nanopore sequence read simulator

adapter trimmer for Oxford Nanopore reads

A comparison of different Oxford Nanopore basecallers

The Biological Observation Matrix (BIOM) Format Project

VirFinder: a novel k-mer based tool for identifying viral sequences from assembled metagenomic data

repository for student workshop pages

Documentation for setting up OpenAPS

Go library for accessing the GitHub API

Java utilities for Bioinformatics

Data intensive science for everyone.

Crafter CMS documentation

The source code that powers readthedocs.org

Bayesian haplotype-based mutation calling

My java Sandbox

Metagenomic binning suite

A single molecule sequence assembler for genomes large and small.

Bring data to life with SVG, Canvas and HTML. 📊📈🎉

Repository for version control of the BrAPI specifications

Notes from books and other interesting things that I've read.

A toolbox for comparative genomics.

Python package for common tasks in bioinformatic.

Reference-free variant discovery in large eukaryotic genomes

Scripts for assembly of PE Illumina from pooled BAC/FACs

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

expVIP. EXPression and VIsualisation Platform

Line-by-line profiling for Python

Genome annotation editor with a Java Server backend and a Javascript client that runs in a web browser as a JBrowse plugin.