HiC-Pro: an optimized and flexible pipeline for Hi-C data processing. Issue 1 (December 2015)
- Record Type:
- Journal Article
- Title:
- HiC-Pro: an optimized and flexible pipeline for Hi-C data processing. Issue 1 (December 2015)
- Main Title:
- HiC-Pro: an optimized and flexible pipeline for Hi-C data processing
- Authors:
- Servant, Nicolas
Varoquaux, Nelle
Lajoie, Bryan
Viara, Eric
Chen, Chong-Jian
Vert, Jean-Philippe
Heard, Edith
Dekker, Job
Barillot, Emmanuel - Abstract:
- Abstract HiC-Pro is an optimized and flexible pipeline for processing Hi-C data from raw reads to normalized contact maps. HiC-Pro maps reads, detects valid ligation products, performs quality controls and generates intra- and inter-chromosomal contact maps. It includes a fast implementation of the iterative correction method and is based on a memory-efficient data format for Hi-C contact maps. In addition, HiC-Pro can use phased genotype data to build allele-specific contact maps. We applied HiC-Pro to different Hi-C datasets, demonstrating its ability to easily process large data in a reasonable time. Source code and documentation are available athttp://github.com/nservant/HiC-Pro .
- Is Part Of:
- Genome biology. Volume 16:Issue 1(2015)
- Journal:
- Genome biology
- Issue:
- Volume 16:Issue 1(2015)
- Issue Display:
- Volume 16, Issue 1 (2015)
- Year:
- 2015
- Volume:
- 16
- Issue:
- 1
- Issue Sort Value:
- 2015-0016-0001-0000
- Page Start:
- 1
- Page End:
- 11
- Publication Date:
- 2015-12
- Subjects:
- Chromosome conformation -- Hi-C -- Bioinformatics pipeline -- Normalization
Genomes -- Periodicals
Biology -- Periodicals
Molecular biology -- Periodicals
572.8633 - Journal URLs:
- http://www.genomebiology.com ↗
http://link.springer.com/ ↗ - DOI:
- 10.1186/s13059-015-0831-x ↗
- Languages:
- English
- ISSNs:
- 1474-760X
- Deposit Type:
- Legaldeposit
- View Content:
- Available online (eLD content is only available in our Reading Rooms) ↗
- Physical Locations:
- British Library DSC - BLDSS-3PM
British Library HMNTS - ELD Digital store - Ingest File:
- 9807.xml