ConDeTri statistics

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Citations per year

Number of citations per year for the bioinformatics software tool ConDeTri
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Tool usage distribution map

This map represents all the scientific publications referring to ConDeTri per scientific context
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Associated diseases

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Popular tool citations

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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

 (58)
library_books

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

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

[…] 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 a […]

library_books

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

2018
Sci Rep
PMCID: 5844893
PMID: 29523860
DOI: 10.1038/s41598-018-22753-4

[…] ts 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 estimatio […]

call_split

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

2018
PLoS One
PMCID: 5755769
PMID: 29304093
DOI: 10.1371/journal.pone.0189738
call_split See protocol

[…] ted 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 with the Pacifi […]

library_books

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

2018
BMC Genomics
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 an in […]

library_books

Modularity Facilitates Flexible Tuning of Plastic and Evolutionary Gene Expression Responses during Early Divergence

2017
Genome Biol Evol
PMCID: 5758911
PMID: 29293993
DOI: 10.1093/gbe/evx278

[…] g the FastQC (v. 0.11.2) quality control tool for sequencing data (). Analysis of the raw reads indicated the presence of low-quality bases in the 3′ end of the reads and an excess of PCR duplicates. ConDeTri read trimmer with default parameters was used to remove low-quality bases and PCR duplicates (). A de novo transcriptome assembly was reconstructed using all nine sequencing libraries (altoge […]

library_books

The draft genome of the hyperthermophilic archaeon Pyrodictium delaneyi strain hulk, an iron and nitrate reducer, reveals the capacity for sulfate reduction

2017
Stand Genomic Sci
PMCID: 5556600
PMID: 28814988
DOI: 10.1186/s40793-017-0260-4

[…] mics core. These libraries were sequenced on an Illumina MiSeq (Illumina, San Diego, CA) using MiSeq Reagent kit v2. The read data from each of the three libraries were trimmed using fastq-mcf [] and ConDeTri [] and analyzed with the genome assembly program Velvet [] to generate three independent draft de novo genome assemblies. A consensus assembly was then generated using Mix [] with a minimum a […]


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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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