FREEC | Copy number and genotype annotation | Genomics library

FREEC is a C++ library typically used in Artificial Intelligence, Genomics applications. FREEC has no bugs, it has no vulnerabilities and it has low support. You can download it from GitHub.

Copy number and genotype annotation from whole genome and whole exome sequencing data. Control-FREEC is a tool for detection of copy-number changes and allelic imbalances (including LOH) using deep-sequencing data originally developed by the Bioinformatics Laboratory of Institut Curie (Paris). Since 2016, the project has moved to Insitut Cochin, INSERM U1016 (Paris). Control-FREEC automatically computes, normalizes, segments copy number and beta allele frequency (BAF) profiles, then calls copy number alterations and LOH. The control (matched normal) sample is optional for whole genome sequencing data but mandatory for whole exome or targeted sequencing data. For whole genome sequencing data analysis, the program can also use mappability data (files created by GEM). Starting from version 8.0, we provide a possibility to detect subclonal gains and losses and evaluate the likeliest average ploidy of the sample. Also, the evaluation procedure for the level of contamination by normal cells has been improved. Input for CNA detection: aligned single-end, paired-end or mate-pair data in SAM, BAM, SAMtools pileup. Control-FREEC accepts .GZ files. Support of Eland, BED, SOAP, arachne, psl (BLAT) and Bowtie formats has been discontinued starting from version 8.0. Input for CNA+LOH detection: There are two options: (a) provide aligned reads in SAMtools pileup format. Files can be GZipped; (b) provide BAM files together with options "makePileup" and "fastaFile" (see "How to create a config file?" in the manual.). Output: Regions of gains, losses and LOH, copy number and BAF profiles. Installation: To install FREEC, type "make" in the command line. If you are using Linux 32bit, please remove 64bit-tags from the Makefile file before building the program.