CuReSim (Customized Read Simulator) is a customized tool which generates synthetic New-Generation Sequencing reads, supporting read simulation for major letter-base sequencing platforms. CuReSim is developed in Java and is distributed as an executable jar file. Wrappers to integrate CuReSim in Galaxy are also available.
If you use CuReSim, please cite Comparison of mapping algorithms used in high-throughput sequencing: application to Ion Torrent data, Caboche et al. BMC Genomics, 2014, 15:264.
The main features of CuReSim include:
- genome (fasta) or read (fastq) as input file
- choice between several error distributions
- a particular attention has been paid to special cases for which several introduced errors in the same read can result in less number of errors as expected due to compensatory changes
- generation of diagrams to know exactly the simulated error model (R is required)
For more details on algorithms and parameters, see the manual of CuReSim.
Installation and usage
CuReSim does not need installation step but require Java installed on your machine (see Java website for more details on Java). Wrappers to integrate CuReSim in Galaxy are also available in CuReSim_galaxy folder.
To run CuReSim, use the following command line:
java -jar CuReSim.jar [options] -f <input_file> [options]
Version 1.3 is now available (24/06/2015)
- some minor bugs were fixed for random reads
- all temporary files are now written in the same directory than the output file specified with the -o parameter
CuReSim1.3 can be freely downloaded.
- Version 1.2 (08/04/2015)
- minor bugs are fixed
- multi-fasta input is allowed
- user can define the maximum number of Ns allowed per read
CuReSimEval: Evaluation of read mapping quality
This program evaluates the mapping quality for simulated reads simulated by CuReSim.
The main features of CuReSimEval include :
- reads (fastq) and mapping (sam) as input files
- choice between several definitions of mapping correctness
- can be used with a large number of mappers
For more details on algorithms and parameters, see the manual of CuReSimEval.
If you use CuReSimEval, please cite Comparison of mapping algorithms used in high-throughput sequencing: application to Ion Torrent data, Caboche et al. BMC Genomics, 2014, 15:264.
Installation and usage
To run CuReSimEval, use the following command line :
java -jar CuReSimEval.jar [options] -f <fastq_file> -s <sam_file> [options]
CuReSimEval can be freely downloaded.
For questions about CuReSim and CuReSimEval or for bug reports, please contact Ségolène Caboche (segolene.caboche<AT>pasteur-lille.fr)