Transposome statistics

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Associated diseases

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Transposome specifications

Information


Unique identifier OMICS_07464
Name Transposome
Software type Toolkit/Suite
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages Perl
License MIT License
Computer skills Advanced
Stability Stable
Maintained Yes

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Maintainer


  • person_outline S. Evan Staton <>

Publication for Transposome

Transposome in publications

 (2)
PMCID: 5895188
PMID: 29732260
DOI: 10.1002/aps3.1030

[…] reads that cover as little as 1% of the genome size can be used as input to programs like repeatexplorer (available as a free galaxy server at http://www.repeatexplorer.org/; novák et al., ) or transposome (staton and burke, ). random, low‐coverage shotgun reads are clustered by nucleotide similarity and overlap, then annotated against a plant repeat database like repbase […]

PMCID: 5007375
PMID: 27557866
DOI: 10.1038/ncomms12679

[…] these sums, thus reducing the influence of outliers., we randomly subsampled 100,000 paired-end sequences from the raw data for each species using seqtk (https://github.com/lh3/seqtk). we then ran transposome on these data with a merge threshold of 0.0001. all other parameters were defaults. clustered sequences were classified by transposome using the repeat database built from the p. gracilis […]


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Transposome institution(s)
Department of Genetics and Department of Plant Biology, University of Georgia, Athens, GA, USA

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