GenomeTools protocols

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GenomeTools specifications

Information


Unique identifier OMICS_16119
Name GenomeTools
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input format BED, .GFF, .GTF, .GVF
Output format BED, .GFF, .GTF, .GVF
Operating system Unix/Linux, Mac OS, Windows
Programming languages C, C++, Python, Ruby
License Other
Computer skills Advanced
Stability Stable
Requirements
Cygwin
Maintained Yes

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Maintainer


  • person_outline Stefan Kurtz <>

Publication for GenomeTools

GenomeTools in pipeline

2018
PMCID: 5894186
PMID: 29636006
DOI: 10.1186/s12864-018-4616-y

[…] set were run on the genome assembly to asses the amount of conserved eukaryotic genes., a library of repeated elements was created as described in []. repeatmodeler v1.0.8, ltrharvest [] part of genometools v1.5.7 and transposonpsi were used in combination to create a set of putative repeats. elements with only a match against an uniprotkb/swissprot database and not against the database […]


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GenomeTools in publications

 (32)
PMCID: 5960304
PMID: 29717040
DOI: 10.1073/pnas.1721395115

[…] october 2015) as described on the gmod site: (i) repeatmodeler with repeatscout v1.0.5, recon v1.08, repeatmasker version open4.0.5, using repbase version 20140131 () and tandemrepeatfinder; (ii) genometools ltrharvest and ltrdigest (); (iii) mitehunter with default parameters (). we generated species-specific repeat libraries for p. andersonii and t. orientalis separately and combined […]

PMCID: 5913888
PMID: 29685100
DOI: 10.1186/s12864-018-4680-3

[…] rmblastn version 2.2.27+ on repbase [] rm database version 20,150,807 (taxon = fungi). de novo repeat families were identified using repeatscout version 1.0.5 []. ltr regions were identified using genometools, suffixerator, ltrharvest (genometools) v1.5.1 (minimum distance 200 bp and maximum distance 5000) and ltrdigest (genometools) v1.5.1 []., de novo repeat families were searched […]

PMCID: 5915480
PMID: 29720997
DOI: 10.3389/fgene.2018.00130

[…] the pipeline is available at http://doi.org/10.5281/zenodo.1098651., long terminal repeat (ltr) elements were detected using two parallel runs of the ltr harvest () and ltrdigest () packages from genometools v1.5.8 (). recent insertions of ltr elements were detected by setting the similarity cutoff in ltr harvest to 99% and only including repeats with a tgca palindromic motif sequence. […]

PMCID: 5894186
PMID: 29636006
DOI: 10.1186/s12864-018-4616-y

[…] set were run on the genome assembly to asses the amount of conserved eukaryotic genes., a library of repeated elements was created as described in []. repeatmodeler v1.0.8, ltrharvest [] part of genometools v1.5.7 and transposonpsi were used in combination to create a set of putative repeats. elements with only a match against an uniprotkb/swissprot database and not against the database […]

PMCID: 5940159
PMID: 29602812
DOI: 10.1534/g3.118.200154

[…] with kimura substitution model and 2000 bootstrap replicates. the phylogenetic tree image was generated using itol version 3 (). gene model tracks (; ) were generated using genometools ()., the raw illumina and pacbio reads from the genomic dna sequencing were submitted to the national center for biotechnology information (ncbi) short read archive (sra) database […]


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GenomeTools institution(s)
Center for Bioinformatics, University of Hamburg, Hamburg, Germany

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