A code-searching tool similar to ack, but faster.

C in four functions

A standalone and lightweight C library

Yank terminal output to clipboard

Full vim for your shell (bash, zsh, gdb, python, etc)

SRA Tools

BWK awk modified for biological data

lumpy: a general probabilistic framework for structural variant discovery

A flexible framework for rapid genome analysis and interpretation

UCSC Genome Browser source. "beta" is released version / "master" is testing.

Program for aligning DNA sequences, a pairwise aligner.

Interval data structure

NCLS. Basically a static interval-tree that is silly fast for both construction and lookups. Deprecated but maintained.

Fast multi-line FASTA/Q reader in several programming languages

Display real time statistics of whatever you want.

Basic operations on the space of numerical functions defined on the genome using lazy evaluators for flexibility and efficiency

PAired-eND Assembler for DNA sequences

A genotype query interface.

shell tools for processing phylogenetic trees

LoFreq Star: Sensitive variant calling from sequencing data

BAMscale is a one-step tool for either 1) quantifying and normalizing the coverage of peaks or 2) generated scaled BigWig files for easy visualization of commonly used DNA-seq capture based methods.

Exascale Maximum Likelihood (ExaML) code for phylogenetic inference using MPI

Position-wise analysis of sequencing and genomics data

The Dazzler Data Base

python wrapper to dpryan79's bigwig library using cffi

apache2 modules for bioinformatics.

Fast but inaccurate adapter trimmer for Illumina reads

a lightweight panel/taskbar, with patches

NeatFreq/Automaton Reference-Free Coverage Reduction Distribution Package

ChIP-seq discretization and quality control