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cookiecutter-cms

Python-centric Cookiecutter for Molecular Computational Chemistry Packages

cosmic2vcf

Convert various TSV files from the Catalogue of Somatic Mutations in Cancer to VCF (esp. structural variants)

covid-gene-expression

Hackathon team: gene expression analysis for Covid-19

cpp-taskflow

Fast C++ Parallel Programming with Task Dependencies

cromrunner

A scheduler / meta-manager for running multiple Cromwell instances on a single WDL workflow in parallel.

cromwell-accountant

A script to calculate estimated cost of a Cromwell workflow on Google Cloud

cromwellonazure

Microsoft Genomics supported implementation of the Broad Institute's Cromwell workflow engine on Azure

cudf

cuDF - GPU DataFrame Library

cutesv

Long read based human genomic structural variation detection with cuteSV

cxxopts

Lightweight C++ command line option parser

cytoscapedev

cytoscapeexperimental

dawdl

WDL library for common bioinformatics tasks

delly

DELLY2: Structural variant discovery by integrated paired-end and split-read analysis

digestpp

C++11 header-only message digest library

discohash

:dancers: Discohash - A super fast and simple hash. 5GB/s serial (depending on hardware).

docker-kraken2

Kraken2 with reference database

dsub

Open-source command-line tool to run batch computing tasks and workflows on backend services such as Google Cloud.

easel

Sequence analysis library used by Eddy/Rivas lab code

emu

An Expectation-Maximization algorithm to infer mutational signatures

enformer-pytorch

english-words

:memo: A text file containing 479k English words for all your dictionary/word-based projects e.g: auto-completion / autosuggestion

fastahack

utilities for indexing and sequence extraction from FASTA files

fe

A python script/minimal GUI app for aggregating variant annotations and predicting impacts

fermi-lite

Standalone C library for assembling Illumina short reads in small regions

firecloud-tools

Dockerfiles and WDL descriptions for various tools on Broad FireCloud

firehose

A collection of scripts for munging genomic and epigenetic data from the Broad Firehose.

fpa

Filter of Pairwise Alignement

freebayes

Bayesian haplotype-based genetic polymorphism discovery and genotyping.

fvr