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cancerlocator

A Java package for non-invasive cancer diagnosis using methylation profiles of cell-Free DNA.

cfdname

cfdnapipe

cfDNApipe: A comprehensive quality control and analysis pipeline for cell-free DNA high-throughput sequencing data

cgmaptools

toolbox for analysing BS-seq data, advance features in SNV, ASM and DMR

cgranges

A C/C++ library for fast interval overlap queries (with a "bedtools coverage" example)

check-sex

Determine the biological sex of a human whole-genome BAM file

chiron

A basecaller for Oxford Nanopore Technologies' sequencers

cnaclinic

cnndel

SV (deletion) detection tool

cnvkit

Copy number variant detection from targeted DNA sequencing

conpair

Concordance and contamination estimator for tumor–normal pairs

conta

Conta is an R package to detect cross contamination and source of contamination

copywriter

DNA copy number detection from off-target sequence data

corenup-datasets

A Combination of Convolutional and Recurrent Deep Neural Networks for NucleosomePositioning Identification

cpplowess

A pure C++ implementation of the lowess algorithm using templates

crag

De novo characterization of cell-free DNA fragmentation hotspots

cragr

R package for CRAG

dangertrack

debruijn-assembly

Practical: genome assembly using De Bruijn graphs

decoder

decode your genome

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.

delfi_scripts

detin

DeTiN is designed to measure tumor-in-normal contamination and improve somatic variant detection sensitivity when using a contaminated matched control.

docker-bam_readcount_helper-cwl

dorado

Oxford Nanopore's Basecaller

droid-sans-mono-zeromod

'Droid Sans Mono' font modified with a dotted or a slashed zero

ebcall

an empirical Bayesian framework for mutation detection from cancer genome sequencing data

ecworkflows

Sequencing Workflows

elprep

elPrep: a high-performance tool for preparing sequence alignment/map files in sequencing pipelines.