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affy2sv

Structural variants calling for Affymetrix Arrays

array-as-vcf

arriba

Fast and accurate gene fusion detection from RNA-Seq data

ascat

ASCAT copy number R package

base

bismark

A tool to map bisulfite converted sequence reads and determine cytosine methylation states

bwa-mem2

The next version of bwa-mem

bwa-meme

Faster BWA-MEM2 using learned-index

cgppindel

Cancer Genome Project Insertion/Deletion detection pipeline based around Pindel

cgpvcf

Vcf file utilities

chromosight

Computer vision based program for pattern recognition in chromosome (Hi-C) contact maps

cis-x

Search for activating regulatory variants in the tumor genome

cyvcf2

cython + htslib == fast VCF and BCF processing

facets

Algorithm to implement Fraction and Copy number Estimate from Tumor/normal Sequencing.

fanc

FAN-C: Framework for the ANalysis of C-like data

fastqsplitter

Splits fastq files evenly

fishplot

Create timecourse "fish plots" that show changes in the clonal architecture of tumors

fithic

Fit-Hi-C is a tool for assigning statistical confidence estimates to chromosomal contact maps produced by genome-wide genome architecture assays such as Hi-C.

g3lollipop.js

Lollipop-diagram to visualize genomic mutations

g3viz

Lollipop-diagram to interactively visualize genetic mutations

gatk

Official code repository for GATK versions 4 and up

ginkgo

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

gridss

GRIDSS: the Genomic Rearrangement IDentification Software Suite

gridss-purple-linx

Standalone GRIDSS/PURPLE/LINX pipeline

gtc2vcf

Tools to convert Illumina IDAT/BPM/EGT/GTC and Affymetrix CEL/CHP files to VCF

hmftools

Various algorithms for analysing genomics data

hmmcopy_utils

Tools for extracting read counts and gc and mappability statistics in preparation for running HMMCopy.

humanidiogramlibrary

Resource of human chromosome schematics & images

igcaller

Python program designed to reconstruct immunoglobulin gene rearrangements and oncogenic translocations from WGS, WES and capture NGS in lymphoid neoplasms.

manta

Structural variant and indel caller for mapped sequencing data