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GSR: Simulator - bmsim
| Attribute | Value |
|---|---|
| Title | bmsim |
| Short Description | BioNano Molecule SIMulator |
| Long Description | BioNano Molecule SIMulator (BMSIM) explicitly incorporated BioNano data models (BioNano molecule length distribution, FN and FP signals, DNA molecules stretching variations, variation in optical resolution, and fragile sites) and the methods to generate chimeric molecules and assign SNR scores for simulated BioNano molecules. We simulated noisy maps from ‘perturbed’ versions of the reference map. Using genomic sequences (.fasta file) as input, BMSIM simulated noisy maps with five main steps: I) generate BioNano molecules with random fragmentation and fragile site bias model; II) abel nicking sites for BioNano molecules by in silico restriction digestion.Our program supported all available nicking enzymes currently used in BioNano systerm (i.e., Nt.BspQI, Nb.BbvCI, Nb.Bsml and Nb.BsrDI), as well as any artificial nicking sequences that users chose to define; III) incorporate data models for FN sites, FP sites, stretching variations, optical resolution, and chimerism for BioNano molecules; IV) assign SNR and intensity scores for labelling sites; V) iterate for targeted coverage depth. The output of BMSIM is a BNX format text file (.BNX, see example BNX file) which contains molecule map length, label positions, and label signal score, ect. |
| Last Release | 6 years, 4 months ago |
| Homepage | https://github.com/pingchen09990102/BMSIM |
| Citations | Chen P, Jing X, Ren J, Cao H, Hao P, Li X, Modelling BioNano optical data and simulation study of genome map assembly., Bioinformatics, Dec. 1, 2018 [ Abstract, cited in PMC ] |
| GSR Certification | ✔ Accessibility |
| Last evaluated | June 22, 2021 (1521 days ago) |
| Author verification | The basic description provided was derived from a website or publications by the GSR team and has not yet been verified by the simulation author. To modify this entry or add more information, propose changes to this simulator. |
| Attribute Category | Attribute |
|---|---|
| Target | |
| Type of Simulated Data | Sequencing Reads, |
| Variations | |
| Simulation Method | |
| Input | |
| Data Type | |
| File format | |
| Output | |
| Data Type | |
| Sequencing Reads | Other, |
| File Format | |
| Sample Type | |
| Phenotype | |
| Trait Type | |
| Determinants | |
| Evolutionary Features | |
| Demographic | |
| Population Size Changes | |
| Gene Flow | |
| Spatiality | |
| Life Cycle | |
| Mating System | |
| Fecundity | |
| Natural Selection | |
| Determinant | |
| Models | |
| Recombination | |
| Mutation Models | |
| Events Allowed | |
| Other | |
| Interface | Command-line, |
| Development | |
| Tested Platforms | |
| Language | Perl, |
| License | MIT, |
| GSR Certification | Accessibility, |
Number of Primary Citations: 1
Number of Non-Primary Citations: 0
No example publication using bmsim has been provided.
Please propose new citations if you are aware of publications that use this software.