arq5x

bedtools2

bedtools - the swiss army knife for genome arithmetic

gemini

a lightweight db framework for exploring genetic variation.

lumpy-sv

lumpy: a general probabilistic framework for structural variant discovery

poretools

a toolkit for working with Oxford nanopore data

bedtools

A powerful toolset for genome arithmetic.

grabix

a wee tool for random access into BGZF files.

cyvcf

A fast Python library for VCF files leveraging Cython for speed.

kway-mergesort

A templated C++ API for memory-assisted, k-way merge sorts

bits

BITS: Binary Interval Search

vitae

ascii_plots

Convenience function for quick and dirty data analysis

arq5x.github.io

goleft

goleft is a collection of bioinformatics tools distributed under MIT license in a single static binary

mosdepth

fast BAM/CRAM depth calculation for WGS, exome, or targetted sequencing.

aws-cli

Universal Command Line Interface for Amazon Web Services

CaBagE-manuscript2

covid-19-data

An ongoing repository of data on coronavirus cases and deaths in the U.S.

covviz

calculate and view coverage based variation

cyvcf2

cython + htslib == fast VCF and BCF processing

d4-format

The D4 Quantatative Data Format

ggd-recipes-1

conda recipes for genomic data

giggle

Interval data structure

igv.js

Embeddable genomic visualization component based on the Integrative Genomics Viewer

markdown-cv

a simple template to write your CV in a readable markdown file and use CSS to publish/print it.

mendacity

language-agnostic testing for inheritance models

peddy

genotype :: ped correspondence check, ancestry check, sex check. directly, quickly on VCF

pyd4

The python binding for D4 format

python-giggle

python (cython) wrapper for https://github.com/ryanlayer/giggle for fast interval searching of huge datasets.

samplot

Plot structural variant signals from many BAMs and CRAMs

sketch

C++ Implementations of sketch data structures with SIMD Parallelism, including Python bindings