ConDeTri 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


Add your version

Documentation


Maintainer


  • person_outline Axel Kunstner <>

Publication for ConDeTri

ConDeTri IN pipelines

 (9)
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) [23], removing adaptor contaminated and duplicate reads produced from pcr amplification and condetri (condetri, rrid:scr_011838) [24] 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: 5905561
PMID: 29444297
DOI: 10.1093/gigascience/giy006

[…] was performed using soapfilter (v2.2), a package from soapdenovo2 (soapdenovo2, rrid:scr_014986) [23], removing adaptor contaminated and duplicate reads produced from pcr amplification and condetri (condetri, rrid:scr_011838) [24] 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, and other default […]

2017
PMCID: 5323629
PMID: 28232450
DOI: 10.1128/genomeA.01677-16

[…] 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 (16). cleaned and filtered nuclear reads were assembled de novo using abyss (17). all obtained sequences were aligned and manually reassembled., the hva980811 […]

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 (8). cleaned and filtered nuclear reads were assembled de novo using abyss (9). all obtained sequences were aligned and manually reassembled., the circular […]

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

ConDeTri reviews

star_border star_border star_border star_border star_border
star star star star star

Be the first to review ConDeTri