arq5x

chrom_sweep

Sweep-line algorithm for genomic features. Detect overlaps on large files w/ minimal memory.

gene_lists

List of gene lists for genomic analyses.

bedder-rs

an API for intersections of genomic data

d4-format

The D4 Quantitative Data Format

bedqc

BED QC tool (in the making)

SVAFotate

rd4tools

An R interface to d4tools

pyd4

The python binding for D4 format

sketch

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

STRling

Detect novel (and reference) STR expansions from short-read data

covviz

Multi-sample genome coverage viewer to observe large, coverage-based anomalies alongside annotations and sample metadata

slivar

genetic variant expressions, annotation, and filtering for great good.

duphold

don't get DUP'ed or DEL'ed by your putative SVs.

cloud-blobstore

Simple API that abstracts out differences between the blobstores across different cloud providers.

hts-nim-tools

useful command-line tools written to showcase hts-nim

batchit

simple jobs submission via command-line for AWS batch

indelope

find large indels (in the blind spot between GATK/freebayes and SV callers)

pathoscore

pathoscore evaluates variant pathogenicity tools and scores.

numerical-linear-algebra

Free online textbook of Jupyter notebooks for fast.ai Computational Linear Algebra course

svaba

Structural variation and indel detection by local assembly

vcfanno_lua

Lua annotation scripts for vcfanno

og-aws

📙 Amazon Web Services — a practical guide

saws

A supercharged AWS command line interface (CLI).

ggd-cli

The command-line interface to GGD

ssec2

Stupid Simple Elastic Compute Cloud

ggd-recipes

conda recipes for genomic data

gsort

sort genomic data

crow

Crow is very fast and easy to use C++ micro web framework (inspired by Python Flask)

svv

Stupid Simple Structural Variant View

pileup.js

Interactive in-browser track viewer