ConDeTri protocols

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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

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Maintainer


  • person_outline Axel Kunstner <>

Publication for ConDeTri

ConDeTri in pipelines

 (16)
2018
PMCID: 5844893
PMID: 29523860
DOI: 10.1038/s41598-018-22753-4

[…] 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 […]

2018
PMCID: 5905561
PMID: 29444297
DOI: 10.1093/gigascience/giy006

[…] 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, […]

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 […]

2017
PMCID: 5220608
PMID: 28068903
DOI: 10.1186/s12864-016-3409-4

[…] were trimmed using the casava v1.8.2 software (illumina, inc.). raw reads obtained after rna-seq was filtered to remove the sequencing adaptor and low quality reads, using a customer perl script (condetri: http://code.google.com/p/condetri) with parameters (-hq = 20 -lq = 10 -frac = 0.8 lfrac = 0.1 -minlen = 50 -mh = 5 -ml = 5 -sc = 64) by removing the primer and adapter sequences. then, […]

2017
PMCID: 5331510
PMID: 28183770
DOI: 10.1128/genomeA.01607-16

[…] a bioanalyzer dna 1000 chip (agilent technologies). one microgram of sonicated dna was end repaired, a-tailed, and adaptor ligated, according to the illumina truseq dna preparation protocol, and condetri was implemented for trimming (). cleaned and filtered nuclear reads were assembled de novo using abyss (). all obtained sequences were aligned and manually reassembled., the circular genomic […]


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ConDeTri in publications

 (58)
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 […]

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 […]

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 […]

PMCID: 5758911
PMID: 29293993
DOI: 10.1093/gbe/evx278

[…] 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 […]


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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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