wook2014,wook2014,github

crispresso2

Analysis of deep sequencing data for rapid and intuitive interpretation of genome editing experiments

cromwell

Scientific workflow engine designed for simplicity & scalability. Trivially transition between one off use cases to massive scale production environments

crossmap

CrossMap is a python program to lift over genome coordinates from one genome version to another.

csbfinder

A Java Desktop application with a graphical user interface for the discovery of colinear syntenic blocks across thousands microbial genomes

cudatext

Cross-platform text editor, written in Lazarus

cutadapt

Cutadapt removes adapter sequences from sequencing reads

cutesv

Long read based human genomic structural variation detection with cuteSV

cwltool

Common Workflow Language reference implementation

cyntenator

Cyntenator is a software for identification of conserved syntenic blocks between multiple genomes.

cytoscape

Cytoscape: an open source platform for network analysis and visualization

cytotree

A Toolkit for Construct Tree-shaped Trajectory for Flow and Mass Cytometry data

dada2

Accurate sample inference from amplicon data with single nucleotide resolution

dagr

A scala based DSL and framework for writing and executing bioinformatics pipelines as Directed Acyclic GRaphs

dashing2

Dashing 2 is a fast toolkit for k-mer and minimizer encoding, sketching, comparison, and indexing.

datahub

A centralized location for storing curated data ready for inclusion in cBioPortal.

DCC uses output from the STAR read mapper to systematically detect back-splice junctions in next-generation sequencing data. DCC applies a series of filters and integrates data across replicate sets to arrive at a precise list of circRNA candidates.

debreak

Structural variant caller for real-time long-read sequencing data

decon

DECoN (Detection of Exon Copy Number) is a sensitive and specific tool for detection of exon copy number variants (exon CNVs) in targeted sequencing data.