bw2

ConfigArgParse

A drop-in replacement for argparse that allows options to also be set via config files and/or environment variables.

ExpansionHunter

A tool for estimating repeat sizes

hail-utils

misc. hail utils

SpliceAI

A deep learning-based tool to identify splice variants

hail-scripts

hail scripts from misc. analyses

REViewer

A tool for visualizing alignments of reads in regions containing tandem repeats

rnaseq-viewer

actions-gh-pages

GitHub Actions for GitHub Pages 🚀 Deploy static files and publish your site easily. Static-Site-Generators-friendly.

annotation-utils

misc. python utilities

bin-utils

Misc. command line utils

bw2.github.io

DeepTrio

DeepTrio tests

deepvariant

DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data.

FRASER

GangSTR

A tool for profiling long STRs from short reads

hail

Scalable genomic data analysis.

igv.js

Embeddable genomic visualization component based on the Integrative Genomics Viewer

impute_sample_metadata

Hail Batch pipelines for imputing the reference genome version, sample type, etc. from BAM or CRAM files.

LIRICAL

LIkelihood Ratio Interpretation of Clinical AbnormaLities

MAPS

code for computing MAPS scores

pandas

Flexible and powerful data analysis / manipulation library for Python, providing labeled data structures similar to R data.frame objects, statistical functions, and much more

Pangolin

Pangolin is a deep-learning method for predicting splice site strengths.

perf

PERF is an Exhaustive Repeat Finder

phaser

phasing and Allele Specific Expression from RNA-seq

popSTR

PopSTR - A Population based microsatellite genotyper

process_profiler

Runs in the background and records telemetry on running processes and system resources. Designed for instrumenting jobs in compute clusters.

pyCircos

python Circos

sma_carrier_detection

step-pipeline

This library is a thin layer over Hail Batch that adds features like skipping steps whose output files have already been generated, additional options for localizing files, notifications on pipeline completion, etc.

STRetch

Method for detecting STR expansions from short-read sequencing data