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G-CNV is a GPU-based tool to prepare sequences for copy number variation (CNV) analysis. This tool filters and masks low-quality reads and nucleotides discard adapter sequences and duplicated reads map and resolve mapping ambiguities compute and normalize read-depth.
Supported GPUs: CUDA enabled NVIDIA (kepler), cc 3.5.


Sequence analysis


  • Operation: Sequence alignment analysis; mapping; sequencing quality control; filtering
  • Input: FASTA; FASTQ
  • Output: -
  • Software interface: Command-line user interface
  • Language: Compiled binary
  • Operating system: Linux
  • License: Not stated
  • Cost: Free
  • Version name: 101
  • Credit: Italian Ministry of Education, the Flagship InterOmics (PB05) and HIRMA (RBAP11YS7K) projects, and the European MIMOmics (305280) project.
  • Contact: andrea.manconi _at_
  • Collection: -


Manconi A, Manca E, Moscatelli M, Gnocchi M, Orro A, Armano G, Milanesi L "G-CNV: A GPU-Based Tool for Preparing Data to Detect CNVs with Read-Depth Methods." Front Bioeng Biotechnol. 2015 Mar 10;3:28.
PMID: 25806367
PMCID: PMC4354384

Download and documentation

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