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FlowSim specifications

Information


Unique identifier OMICS_00250
Name FlowSim
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
License GNU General Public License version 2.0
Computer skills Advanced
Stability Stable
Maintained Yes

Versioning


No version available

Publication for FlowSim

FlowSim citations

 (5)
library_books

Best practices for evaluating single nucleotide variant calling methods for microbial genomics

2015
Front Genet
PMCID: 4493402
PMID: 26217378
DOI: 10.3389/fgene.2015.00235

[…] is more representative of the distribution of quality scores in a sequencing dataset, it assumes the quality scores are accurate.The assigned BQS can also reflect the model uncertainty. For example, flowsim () uses Bayes theorem to assign quality values for simulated base calls. takes the opposite approach, modeling quality scores and using those assigned quality scores for the base call error m […]

library_books

Estimating the information value of polymorphic sites using pooled sequences

2014
BMC Genomics
PMCID: 4239578
PMID: 25571927
DOI: 10.1186/1471-2164-15-S6-S20

[…] A set of simulated reads were generated using FlowSim [], using a procedure adapted to populations genetics studies []. A section of 10 megabases, comprised of the four largest scaffolds, was extracted from the salmon louse (Lepeophtheirus salmon […]

library_books

Simulating a population genomics data set using FlowSim

2014
BMC Res Notes
PMCID: 3942619
PMID: 24479665
DOI: 10.1186/1756-0500-7-68

[…] ally targeting specific data types or analyses. For instance, MetaSim [] targets metagenomic samples, and SimSeq (St. John, unpublished) and Wgsim [] target Illumina sequences.As implied by the name, FlowSim [] was originally developed for simulation of de novo genomics data on the 454 platform. Since its inception, it has grown into a flexible suite of tools that can be applied to a number of dif […]

library_books

A cost effective and universal strategy for complete prokaryotic genomic sequencing proposed by computer simulation

2012
BMC Res Notes
PMCID: 3296665
PMID: 22289569
DOI: 10.1186/1756-0500-5-80

[…] Metasim and Flowsim are both pyrosequencing simulators, which generate pyrosequencing reads in different manners. Metasim is based on parametric model, while Flowsim is based on empirical model which is much more […]

library_books

Systematic exploration of error sources in pyrosequencing flowgram data

2011
Bioinformatics
PMCID: 3117331
PMID: 21685085
DOI: 10.1093/bioinformatics/btr251

[…] lation, we used a 764 Mb genomic scaffold from sea bass (D.labrax) generated from Sanger sequencing (), where we also had available approximately 30× coverage 454 shotgun reads for comparison.We used flowsim to simulate a high number of reads corresponding to 10× coverage, providing sufficient clone lengths for 800 flows (Titanium), using empirical distributions as flow model and quality degradati […]

Citations

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FlowSim institution(s)
Institute of Marine Research, University of Bergen, Bergen, Norway

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