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cc2

cnvkit

Copy number variant detection from targeted DNA sequencing

cnvnator

a tool for CNV discovery and genotyping from depth-of-coverage by mapped reads

conpair

Concordance and contamination estimator for tumor–normal pairs

copy-number-analysis

Explore, compare, and evaluate Bioconductor packages related to genomic copy number analysis

cromwell

Workflow Execution Engine using WDL

ctcnv

A new CNV calling method for DNA-seq data

cutadapt

cutadapt removes adapter sequences from sequencing reads

dash

Analytical Apps for Python. Dash Is Productive™

data-science

:bar_chart: Path to a free self-taught education in Data Science!

deeplearning-biology

A list of deep learning implementations in biology

deeptools

Tools to process and analyze deep sequencing data.

deepvariant

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

denovotargetcapturepopgen

Bioinformatics pipelines for processing transciptome-based exon capture data in population genomic analyses

dna-seq-analysis

my notes on whole exome and whole genome sequencing analysis

fgbio

Tools for working with genomic and high throughput sequencing data.

fqc

Extensible quality control dashboard built around FASTQ assessment.

freebayes

Bayesian haplotype-based genetic polymorphism discovery and genotyping.

fsda

ga4gh-schemas

Models and APIs for Genomic data. RETIRED 2018-01-24

galaxy

Data intensive science for everyone.

gatk

Official code repository for GATK versions 4 and up

gatk-pipeline

A shell script which implements GATK pipeline for variant calling.

gatk4-somatic-snvs-indels

Workflows for somatic short variant discovery with GATK4

genomic_purity

characterization of test material purity using whole genome sequencing data

getting-started-with-genomics-tools-and-resources

Unix, R and python tools for genomics

ginkgo

Cloud-based single-cell copy-number variation analysis tool

git_learn

gitaxidisvert

hgvs

Python library to parse, format, validate, normalize, and map sequence variants. `pip install hgvs`