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Protocols

ConDeTri specifications

Information


Unique identifier OMICS_01085
Name ConDeTri
Software type Package/Module
Interface Command line interface
Restrictions to use None
Biological technology Illumina
Operating system Unix/Linux
License Artistic License version 2.0, GNU General Public License version 2.0
Computer skills Advanced
Stability Stable
Maintained Yes

Versioning


No version available

Documentation


Maintainer


  • person_outline Axel Kunstner <>

Publication for ConDeTri

ConDeTri citations

 (68)
library_books

Acquisition and dissemination of cephalosporin resistant E. coli in migratory birds sampled at an Alaska landfill as inferred through genomic analysis

2018
PMCID: 5943298
PMID: 29743625
DOI: 10.1038/s41598-018-25474-w

[…] using the miseq platform (illumina, san diego, usa) using either 250 or 300 base pair read lengths. average read depth was determined by reference mapping to the e. coli k12 genome (nc_000913.3)., condetri was used to remove reads with low quality scores, trim high quality reads and remove duplicate reads. high-quality, trimmed, unique reads were assembled with spades using default parameters […]

call_split

Allele specific expression in a family quartet with autism reveals mono to biallelic switch and novel transcriptional processes of autism susceptibility genes

2018
PMCID: 5844893
PMID: 29523860
DOI: 10.1038/s41598-018-22753-4
call_split See protocol

[…] to create haploid genomic sequences for the parents and offspring based on the human reference genome grch38. for rna-seq analysis, the sequences generated were filtered to obtain qualified reads. condetri was implemented to trim or remove the reads according to the quality score. qualified reads after filtering low-quality data were analyzed using tophat/cufflinks for gene expression […]

library_books

Optimized Method of Extracting Rice Chloroplast DNA for High Quality Plastome Resequencing and de Novo Assembly

2018
PMCID: 5835797
PMID: 29541088
DOI: 10.3389/fpls.2018.00266

[…] on the nig supercomputer at the rois national institute of genetics., https://www.ncbi.nlm.nih.gov/genome/browse/?report=5 , http://broadinstitute.github.io/picard/ , https://github.com/linneas/condetri , the supplementary material for this article can be found online at: […]

call_split

Draft genomes of two blister beetles Hycleus cichorii and Hycleus phaleratus

2018
PMCID: 5905561
PMID: 29444297
DOI: 10.1093/gigascience/giy006
call_split See protocol

[…] control was performed using soapfilter (v2.2), a package from soapdenovo2 (soapdenovo2, rrid:scr_014986) [], removing adaptor contaminated and duplicate reads produced from pcr amplification and condetri (condetri, rrid:scr_011838) [] to trimming low-quality bases, with the following parameters: -rmn, -hq = 20, -lq = 10, -frac = 0.8, -lfrac = 0.1, -minlen = 90, -mh = 5, -ml = 5, […]

library_books

The genomes of Crithidia bombi and C. expoeki, common parasites of bumblebees

2018
PMCID: 5755769
PMID: 29304093
DOI: 10.1371/journal.pone.0189738

[…] and sequenced four fragment libraries, producing 65,082,902 single-end reads of 76 bp length. reads containing adapters were trimmed with cutadapt []. quality-filtering and trimming was done with condetri.pl []. we used the illumina reads to error-correct the pacbio reads with the pacbiotoca module of the wgs-assembler version 7., we sequenced the full genome of crithidia expoeki […]

library_books

Analysis of the hybrid genomes of two field isolates of the soil borne fungal species Verticillium longisporum

2018
PMCID: 5753508
PMID: 29298673
DOI: 10.1186/s12864-017-4407-x

[…] strand-specific sequencing of the mrna libraries at scilife lab, stockholm (sweden). libraries were prepared by the sequencing platform under their in-house conditions. after quality filtering using condetri v2.2 [] 113.8 and 84.08 millions high quality paired-end reads remained for vl1 and vl2, respectively. these reads were mapped to the de novo assemblies using tophat v2.0.9 [], assuming […]


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ConDeTri institution(s)
Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden
ConDeTri funding source(s)
Supported by the Swedish Research Council.

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