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454sim specifications


Unique identifier OMICS_06832
Name 454sim
Software type Package/Module
Interface Command line interface
Restrictions to use None
Biological technology Roche
Operating system Unix/Linux, Windows
Programming languages C++
Computer skills Advanced
Stability Stable
Maintained Yes


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Publication for 454sim

454sim citations


A Comparison of Methods for Clustering 16S rRNA Sequences into OTUs

PLoS One
PMCID: 3742672
PMID: 23967117
DOI: 10.1371/journal.pone.0070837

[…] we generated ten 16s rrna simulated datasets (simclone10_1, simclone10_2, simclone15_1, simclone15_2 and simclone20, simclone30, simclone50, simclone100, simclone150, simclone200) using the software 454sim , which simulates 454 data using configurable statistical models that can accommodate different number of sequence reads, sequence lengths, errors rates, and abundance. provides the detailed […]


Highly improved homopolymer aware nucleotide protein alignments with 454 data

BMC Bioinformatics
PMCID: 3568017
PMID: 22971057
DOI: 10.1186/1471-2105-13-230

[…] the corresponding blosum(x) substitution probabilities [], where x denotes the clustering identity threshold used. in order to supply query sequences, 1,000 454 titanium reads were simulated by the “454sim” simulator [], using default settings. finally, 4216 parameter combinations were evaluated for all seven degrees of difficulty, by alignment of the 1,000 reads to each of the seven target […]

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454sim institution(s)
IFM Bioinformatics and SeRC (Swedish e-Science Research Centre), Linköping University, Linköping, Sweden

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