simNGS statistics

info info

Citations per year

info

Popular tool citations

chevron_left Read simulation chevron_right
info

Tool usage distribution map

Tool usage distribution map
info info

Associated diseases

Associated diseases
Want to access the full stats & trends on this tool?

Protocols

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

Versioning


No version available

Documentation


Maintainer


  • person_outline Nick Goldman

simNGS citations

 (4)
library_books

Extension of the viral ecology in humans using viral profile hidden Markov models

2018
PLoS One
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 […]

library_books

Landscape of tumor infiltrating T cell repertoire of human cancers

2016
Nat Genet
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 […]

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

[…] 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/ , […]

library_books

An Improved Protocol for Sequencing of Repetitive Genomic Regions and Structural Variations Using Mutagenesis and Next Generation Sequencing

2012
PLoS One
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 […]


Want to access the full list of citations?

simNGS reviews

star_border star_border star_border star_border star_border
star star star star star

Be the first to review simNGS