Purdue University

CONCOCT: Clustering cONtigs with COverage and ComposiTion.

Control-freec is a tool for detection of copy-number changes and allelic imbalances (including LOH) using deep-sequencing data.

Cooler is a support library for a sparse, compressed, binary persistent storage format, also called cooler, used to store genomic interaction data, such as Hi-C contact matrices.

CosmosScope is a graphical waveform analyzer tool that allows you to view and analyze simulation results in the form of waveforms displayed on graphs, or as values displayed in lists.

Coverm is a configurable, easy to use and fast DNA read coverage and relative abundance calculator focused on metagenomics applications.

Covgen creates a target specific exome_full192.coverage.txt file required by MutSig.

CP2K is a quantum chemistry and solid state physics software package that can perform atomistic simulations of solid state, liquid, molecular, periodic, material, crystal, and biological systems.

IBM ILOG CPLEX Optimizer's mathematical programming technology enables decision optimization for improving efficiency, reducing costs, and increasing profitability.

Cramino is a tool for quick quality assessment of cram and bam files, intended for long read sequencing.

CRISPRCasFinder enables the easy detection of CRISPRs and cas genes in user-submitted sequence data. It is an updated, improved, and integrated version of CRISPRFinder and CasFinder.

CRISPResso2 is a software pipeline designed to enable rapid and intuitive interpretation of genome editing experiments.

Crispritz is a software package containing 5 different tools dedicated to perform predictive analysis and result assessment on CRISPR/Cas experiments.

Crossmap is a program for genome coordinates conversion between different assemblies.

cross_match is a general purpose utility for comparing any two DNA sequence sets using a 'banded' version of swat.

csvkit is a suite of command-line tools for converting to and working with CSV, the king of tabular file formats.

Csvtk is a cross-platform, efficient and practical CSV/TSV toolkit.

CUDA is a parallel computing platform and programming model invented by NVIDIA. It enables dramatic increases in computing performance by harnessing the power of the graphics processing unit (GPU).

cuDNN is a deep neural network library from Nvidia that provides a highly tuned implementation of many functions commonly used in deep machine learning applications.

Cufflinks assembles transcripts, estimates their abundances, and tests for differential expression and regulation in RNA-Seq samples. It accepts aligned RNA-Seq reads and assembles the alignments into a parsimonious set of transcripts. Cufflinks then estimates the relative abundances of these transcripts based on how many reads support each one, taking into account biases in library preparation protocols.

cURL is an open source command line tool and library for transferring data with URL syntax.