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Protocols

Gepard specifications

Information


Unique identifier OMICS_09603
Name Gepard
Alternative name GEnome PAir - Rapid Dotter
Software type Package/Module
Interface Graphical user interface
Restrictions to use None
Operating system Unix/Linux
Programming languages Java
Computer skills Medium
Version 1.30
Stability Stable
Maintained Yes

Versioning


No version available

Maintainer


  • person_outline Jan Krumsiek <>

Publication for GEnome PAir - Rapid Dotter

Gepard citations

 (121)
call_split

Phages infecting Faecalibacterium prausnitzii belong to novel viral genera that help to decipher intestinal viromes

2018
PMCID: 5883640
PMID: 29615108
DOI: 10.1186/s40168-018-0452-1
call_split See protocol

[…] of the ncbi by blastn, with the discontinuous megablast default parameters. sequences producing alignments covering more than 5% of the query were retained. whole genome dotplots were realized with gepard [], using a length of 11 nt for minimal exact matches. crispr spacers were searched for with crisprdetect [], using default parameters., for each prophage pair to be compared, all proteins […]

library_books

Sequencing and Analysis of Strobilanthes cusia (Nees) Kuntze Chloroplast Genome Revealed the Rare Simultaneous Contraction and Expansion of the Inverted Repeat Region in Angiosperm

2018
PMCID: 5861152
PMID: 29593773
DOI: 10.3389/fpls.2018.00324

[…] sequence similarity to the reads and was used as a reference for the downstream genome assembly., abyss (v1.5.2) () and clc genomics workbench (v7) was used for the de novo genome assembly. using gepard (), we identified 7 contigs from the assembly of contigs of abyss and clc genomics workbench, respectively, that nearly spanned the entire cp genome. all the 14 contigs were assembled using […]

library_books

Complete Genome Sequence of Escherichia coli ML35

2018
PMCID: 5814495
PMID: 29449382
DOI: 10.1128/genomeA.00034-18

[…] to regions of the large contig. combined with its low coverage, this suggests that the small contig is an assembly artifact; therefore, we discarded it. to circularize the large contig, we used gepard () to visualize overlap between the ends of the contig and blast () and emboss extractseq () to specify coordinates and trim overlap, thereby generating a closed 4,918,091-bp contig., […]

library_books

Complete Genome Sequence of Pseudomonas sp. Strain NC02, Isolated from Soil

2018
PMCID: 5814507
PMID: 29449381
DOI: 10.1128/genomeA.00033-18

[…] process version 3 (hgap3) (), with an estimated genome size of 11 mb and target coverage of 25×. this generated one 6,912,634-bp contig with 132× mean coverage. to circularize the contig, we used gepard () to visualize the overlap between contig ends and blast () and emboss extractseq () to specify coordinates and trim overlap, thereby generating a closed 6,890,354-bp contig., to polish […]

library_books

Genomic Analysis of Hospital Plumbing Reveals Diverse Reservoir of Bacterial Plasmids Conferring Carbapenem Resistance

2018
PMCID: 5801463
PMID: 29437920
DOI: 10.1128/mBio.02011-17

[…] (pacbio smrt analysis version 2.3) or canu (version 1.3, 1.4, or 1.5) (). the resulting contigs were polished by using quiver (smrt analysis version 2.3) and manually reviewed and finished by using gepard (version 1.3) (). base calling and finishing accuracy was assessed by using the most probable genotype () software with illumina miseq read alignments against the finished pacbio assembly. […]

library_books

Multi omics Reveals the Lifestyle of the Acidophilic, Mineral Oxidizing Model Species Leptospirillum ferriphilumT

2018
PMCID: 5772234
PMID: 29150517
DOI: 10.1128/AEM.02091-17

[…] was conducted with hgap3 at the sequencing facility, including quiver for consensus corrections. the large contig was circularized with circlator () after inspection of dot plots produced with gepard (). the −fixstart option was applied to set the dnaa gene as the first gene. prokka v1.12-beta () was used for genome annotation, which included prodigal v2.6.3 () for the prediction […]


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Gepard institution(s)
Institute for Bioinformatics (MIPS), GSF National Research Center for Environment and Health, Ingolstädter, Neuherberg, Germany; Technische Universität München, Department of Genome Oriented Bioinformatics, Freising, Germany

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