simNGS protocols

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simNGS specifications

Information


Unique identifier OMICS_12444
Name simNGS
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input data simNGS takes fasta format sequences and a file describing the covariance of noise between bases and cycles observed in an actual run of the machine, randomly generates noisy intensities representing the signals for the sequence at each cycle and calculates likelihoods for all possible base calls.
Biological technology Illumina
Operating system Unix/Linux, Mac OS
Programming languages C
License GNU General Public License version 3.0
Computer skills Advanced
Stability Stable
Maintained Yes

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  • person_outline Nick Goldman <>

simNGS in pipeline

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

[…] hshqpm-13-x-00190 with nist and hshqdc-10-c-00152 to tgen (keim) and nau (foster)., http://genomeinabottle.org , https://github.com/nate-d-olson/snp_eval_shiny , http://www.ebi.ac.uk/goldman-srv/simngs/ , https://github.com/ekg/mutatrix , https://github.com/chapmanb/bcbio.variation , https://github.com/ekg/vcflib , http://useq.sourceforge.net/ , […]


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simNGS in publications

 (4)
PMCID: 5774701
PMID: 29351302
DOI: 10.1371/journal.pone.0190938

[…] group contained sequences coding for a protein distantly homologous to the satellite tobacco necrosis virus coat protein., in order to evaluate the performance of the viral hmm pipeline, we used simngs and simlibrary (http://www.ebi.ac.uk/goldman-srv/simngs/#about) tools (the default settings of these tools were used) to simulate sequencing reads from 100 000 different genomes from genbank […]

PMCID: 5298896
PMID: 27240091
DOI: 10.1038/ng.3581

[…] council fellowship., urls , cancer genomics hub: https://cghub.ucsc.edu, tcga data portal: https://tcga-data.nci.nih.gov/tcga/tcgadownload.jsp, gdac firehose: https://gdac.broadinstitute.org/, simngs: http://www.ebi.ac.uk/goldman-srv/simngs/, immunoseq data accession: https://adaptivebiotech.com/pub/liu-2016-natgenetics, data accession , immunoseq data generated in this study […]

PMCID: 4493402
PMID: 26217378
DOI: 10.3389/fgene.2015.00235

[…] hshqpm-13-x-00190 with nist and hshqdc-10-c-00152 to tgen (keim) and nau (foster)., http://genomeinabottle.org , https://github.com/nate-d-olson/snp_eval_shiny , http://www.ebi.ac.uk/goldman-srv/simngs/ , https://github.com/ekg/mutatrix , https://github.com/chapmanb/bcbio.variation , https://github.com/ekg/vcflib , http://useq.sourceforge.net/ , […]

PMCID: 3422288
PMID: 22912860
DOI: 10.1371/journal.pone.0043359

[…] is proportional to the number of their descendants after the final pcr; thus we take into account the fluctuation in coverage due to the amplification., we simulated illumina sequencing by using the simngs package version 1.5 , with default parameters and trained on intensity data produced by a paired-end run with a read length of 101 on an illumina hiseq sequencer. the simngs package simulates […]


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