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alignment-and-variant-calling-tutorial

basic walk-throughs for alignment and variant calling from NGS sequencing data

applied-computational-genomics

Applied Computational Genomics Course at UU: Spring 2017

beadarrayfiles

Python library to parse file formats related to Illumina bead arrays

bioawk

BWK awk modified for biological data

canvas

Canvas - Copy number variant (CNV) calling from DNA sequencing data

ccrhtml

A small repo for storing the code for making the files and html for CCRs.

ccs

CCS: Generate Highly Accurate Single-Molecule Consensus Reads (HiFi Reads)

ch-model

This is the repository of CH model.

clair3

Clair3 - Integrating pileup and full-alignment for high-performance long-read variant calling

clump

CLUstering by Mutation Position

cn_learn

CN-Learn

cnvnator

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

conifer-tools

CoNIFER Tools - Tools for improving call generation, annotation and filtering. Used in conjuction with CoNIFER (Copy Number Inference From Exome Reads)

covid-19

Novel Coronavirus (COVID-19) Cases, provided by JHU CSSE

data-access-notebook

Jupyter Notebook that illustrates how to query, package, and download data from NIMH Data Archive

data-science-at-the-command-line

Data Science at the Command Line

dataviz

A book covering the fundamentals of data visualization.

deepvariant

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

denovofilter

Rules for filtering candidate de novo sites

denovonear

analysing proximity clustering of de novo variants in genes

denovowest

doc-annovar

Documentation for the ANNOVAR software

dokuwiki

The DokuWiki Open Source Wiki Engine

drawio

Source to www.draw.io

exomiser

A Tool to Annotate and Prioritize Exome Variants

expansionhunter

A tool for estimating repeat sizes

expansionhunterdenovo

A suite of tools for detecting expansions of short tandem repeats

fastcn

fastqc

A quality control analysis tool for high throughput sequencing data

fastx_toolkit

FASTA/FASTQ pre-processing programs