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Protocols

Tedna specifications

Information


Unique identifier OMICS_12853
Name Tedna
Software type Package/Module
Interface Command line interface
Restrictions to use None
Biological technology Illumina
Operating system Unix/Linux
Programming languages C++
License GNU General Public License version 3.0
Computer skills Advanced
Version 1.2.2
Stability Stable
Requirements
Sparsehash
Maintained Yes

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Documentation


Maintainer


  • person_outline Matthias Zytnicki

Publication for Tedna

Tedna citations

 (8)
library_books

Efficient transgenesis and annotated genome sequence of the regenerative flatworm model Macrostomum lignano

2017
Nat Commun
PMCID: 5730564
PMID: 29242515
DOI: 10.1038/s41467-017-02214-8

[…] Two methods were applied to identify repetitive elements de novo both from the raw sequencing data and from the assembled scaffolds. Tedna software v. 1.2.1 was used to assemble transposable element models directly from the repeated fraction of raw Illumina paired-end sequencing reads with the parameters “-k 31 -i 300 -m 200 -t 37 […]

call_split

Mitochondrial genomes of the key zooplankton copepods Arctic Calanus glacialis and North Atlantic Calanus finmarchicus with the longest crustacean non coding regions

2017
Sci Rep
PMCID: 5651803
PMID: 29057900
DOI: 10.1038/s41598-017-13807-0
call_split See protocol

[…] gene order data was performed using several heuristics implemented in CREx web server. Analysis of k-mer frequency distributions were done in Jellyfish and the assembly of repeatable DNA was done in Tedna , the provisional classification of the assembled elements was done by TEclass. All mapping and manipulation of genomic reads were done in CLC Genomics Workbench. […]

library_books

Running Injuries in the Participants of Ljubljana Marathon

2017
PMCID: 5639808
PMID: 29062393
DOI: 10.1515/sjph-2017-0027

[…] je bil 23,1 kg/m2. Glede na pretečeno razdaljo je bila razporeditev naslednja: maraton 132, polmaraton 412 in tek na 10 km 153 udeležencev. Življenjska incidenca tekaških poškodb (odsotnost s teka 2 tedna ali več) je bila naslednja: 322 (46 %) nikoli, 328 (47 %) redko, 31 (4 %) občasno in 16 (2 %) pogosto. Najpogosteje poškodovani telesni deli so bili: koleno (30 %), gleženj in Ahilova tetiva (24 […]

library_books

Copy number increases of transposable elements and protein‐coding genes in an invasive fish of hybrid origin

2017
Mol Ecol
PMCID: 5638112
PMID: 28390096
DOI: 10.1111/mec.14134

[…] ssible accumulation of TEs in invasive Cottus, we used a genome mapping approach to compare the relative number of reads mapped to a de novo assembly of repetitive elements. The de novo assemblies in tedna resulted in a total of 7,548 sequences, which were assembled in seqman pro into 1,005 contigs (hereafter referred to as “repetitive elements”; size range: 500‐50k bp; n50: 2,978 bp; Table ). Usi […]

library_books

LoRTE: Detecting transposon induced genomic variants using low coverage PacBio long read sequences

2017
Mob DNA
PMCID: 5385071
PMID: 28405230
DOI: 10.1186/s13100-017-0088-x

[…] ] for exhaustive descriptions of the different strategies. Briefly, the first approach is based on the direct assembly of the repeated fraction of the reads using highly abundant k-mer : RepARK [] or Tedna []. Other tools such as RepeatExplorer [] or dnaPipeTE [] used low-coverage sub-samples of the reads in order to retrieve and specifically assemble the highly repeated elements. All these tools […]

library_books

Directional Selection from Host Plants Is a Major Force Driving Host Specificity in Magnaporthe Species

2016
Sci Rep
PMCID: 4858695
PMID: 27151494
DOI: 10.1038/srep25591

[…] For the newly sequenced isolates, a transposable elements assembler based on reads K-mer tool, Tedna was used. Also, we constructed a de novo repeat library for all isolates using RepeatModeler (version 1.0.8) based on assembled genome with the default parameters, which generated consensus sequ […]

Citations

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Tedna institution(s)
INRA, URGI, Plant Breeding and Biology, Versailles, France; Department of Plant Pathology, Kansas State University, Manhattan, KS, USA

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