BSSim
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Application data |
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| Created by | Luke You, Jinyu Wu |
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| Biological application domain(s) | DNA methylation, Sequencing, Epigenetics |
| Principal bioinformatics method(s) | Modelling and simulation |
| Technology | Illumina, 454, ABI SOLiD |
| Created at | Institute of Genomic Medicine, Wenzhou Medical College, Wenzhou 325035, China |
| Maintained? | Yes |
| Input format(s) | FASTA |
| Output format(s) | FASTQ, SAM, Ref |
| Software features | BSSim can allow users to mimic various methylation level. |
| Programming language(s) | Python |
| Licence | GPLv3 |
| Operating system(s) | UNIX, Linux, Mac OS X, Windows |
Summary: BSSim: Bisulfite sequencing simulator for next-generation sequencing.
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Description
BSSim is implemented in the Python language and run in an operating system-independent manner. It can allow users to mimic various methylation level (total methylation level of cytosines, percentage of cytosines that methylated and methylation level of total methylcytosines) and bisulfite conversion rate in CpG, CHG and CHH context, respectively. It can also simulate genetic variations that are divergent from the reference sequence along with the sequencing error and quality distributions. In the output, both directional/non-directional, various read length, single/paired-end reads and alignment data in the SAM format can be generated. BSSim is a cross-platform BS-seq simulator offers output read datasets not only suitable for Illumina's Solexa, but also for Roche's 454 and Applied Biosystems' SOLiD.
Links
References
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