arq5x

og-aws

📙 Amazon Web Services — a practical guide

numerical-linear-algebra

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

crow

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

saws

A supercharged AWS command line interface (CLI).

pileup.js

Interactive in-browser track viewer

slivar

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

svaba

Structural variation and indel detection by local assembly

gene_lists

List of gene lists for genomic analyses.

d4-format

The D4 Quantitative Data Format

sketch

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

duphold

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

ggd-recipes

conda recipes for genomic data

batchit

simple jobs submission via command-line for AWS batch

bedder-rs

an API for intersections of genomic data

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

hts-nim-tools

useful command-line tools written to showcase hts-nim

ggd-cli

The command-line interface to GGD

indelope

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

SVAFotate

gsort

sort genomic data

svv

Stupid Simple Structural Variant View

pathoscore

pathoscore evaluates variant pathogenicity tools and scores.

pyd4

The python binding for D4 format

ssec2

Stupid Simple Elastic Compute Cloud

bedqc

BED QC tool (in the making)

chrom_sweep

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

cloud-blobstore

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

vcfanno_lua

Lua annotation scripts for vcfanno

rd4tools

An R interface to d4tools