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GSR: Simulator - LongISLND
| Attribute | Value |
|---|---|
| Title | LongISLND |
| Short Description | LongISLND is a read simulator which profiles the characteristics of third generation, single-molecule sequencing technologies and simulates accordingly |
| Long Description | LongISLND is a read simulator which profiles the characteristics of third generation, single-molecule sequencing technologies and simulates accordingly. The general software architecture is easily extendable, as demonstrated by the emulation of Pacific Biosciences (PacBio) multi-pass sequencing with P5 and P6 chemistries, producing data in FASTQ, H5, and the latest PacBio BAM format. Please read on to see application examples to PacBio and oxford nanopre (ONT) data. |
| Keywords | PacBio |
| Version | 0.9.6 |
| Project Started | 2017 |
| Last Release | 7 years ago |
| Homepage | https://github.com/bioinform/longislnd |
| Citations | Lau B, Mohiyuddin M, Mu JC, Fang LT, Bani Asadi N, Dallett C, Lam HY, LongISLND: in silico sequencing of lengthy and noisy datatypes., Bioinformatics, 12-15-2016 [ Abstract, cited in PMC ] |
| GSR Certification |  ✔ Accessibility |
| Last evaluated | 10-28-2021 (898 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 | Biallelic Marker, Insertion and Deletion, Missing Genotypes, |
| Simulation Method | |
| Input | |
| Data Type | |
| File format | |
| Output | |
| Data Type | |
| Sequencing Reads | PacBio, |
| File Format | Fasta or Fastq, SAM or BAM, |
| 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 | |
| Development | |
| Tested Platforms | |
| Language | Java, |
| License | Creative Commons, |
| GSR Certification | Accessibility, Documentation, Application, Support, |
Number of Primary Citations: 1
Number of Non-Primary Citations: 2
The following 2 publications are selected examples of applications that used LongISLND.
2021
Ono Y, Asai K, Hamada M, PBSIM2: a simulator for long-read sequencers with a novel generative model of quality scores., Bioinformatics, 05-05-2021 [Abstract]
Dierckxsens N, Li T, Vermeesch JR, Xie Z, A benchmark of structural variation detection by long reads through a realistic simulated model., Genome Biol, 12-15-2021 [Abstract]